ABL_cosmic_analysis

workflowr

• Summary
• Checks
• Past versions

Last updated: 2023-02-24

Checks: 6 1

Knit directory: duplex_sequencing_screen/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: uncommitted changes

The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200402)

The command set.seed(20200402) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 7ac4a41

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 7ac4a41. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

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    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy126-[BamLeftAlign_on_data_125_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy130-[BamLeftAlign_on_data_129_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy130-[BamLeftAlign_on_data_129_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy74-[BamLeftAlign_on_data_73_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy74-[BamLeftAlign_on_data_73_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy78-[BamLeftAlign_on_data_77_(alignments)] (1).bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy78-[BamLeftAlign_on_data_77_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy78-[BamLeftAlign_on_data_77_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy82-[BamLeftAlign_on_data_81_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy82-[BamLeftAlign_on_data_81_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy86-[BamLeftAlign_on_data_85_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy86-[BamLeftAlign_on_data_85_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy90-[BamLeftAlign_on_data_89_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy90-[BamLeftAlign_on_data_89_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy94-[BamLeftAlign_on_data_93_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy94-[BamLeftAlign_on_data_93_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy98-[BamLeftAlign_on_data_97_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane4/GalaxyData/Galaxy98-[BamLeftAlign_on_data_97_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy14-[BamLeftAlign_on_data_13_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy14-[BamLeftAlign_on_data_13_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy18-[BamLeftAlign_on_data_17_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy18-[BamLeftAlign_on_data_17_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy22-[BamLeftAlign_on_data_21_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy22-[BamLeftAlign_on_data_21_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy57-[BamLeftAlign_on_data_56_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy57-[BamLeftAlign_on_data_56_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy61-[BamLeftAlign_on_data_60_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy61-[BamLeftAlign_on_data_60_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy65-[BamLeftAlign_on_data_64_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy65-[BamLeftAlign_on_data_64_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy69-[BamLeftAlign_on_data_68_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy69-[BamLeftAlign_on_data_68_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy73-[BamLeftAlign_on_data_72_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy73-[BamLeftAlign_on_data_72_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy77-[BamLeftAlign_on_data_76_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy77-[BamLeftAlign_on_data_76_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy38-[BamLeftAlign_on_data_37_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy38-[BamLeftAlign_on_data_37_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy42-[BamLeftAlign_on_data_41_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy42-[BamLeftAlign_on_data_41_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bam
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bai
    Deleted:    data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bam
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_Duplex_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_Duplex_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_SSCS_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_SSCS_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_Duplex_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_Duplex_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_SSCS_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_SSCS_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_Duplex_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_Duplex_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_SSCS_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_SSCS_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_Duplex_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_Duplex_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_SSCS_routput.csv
    Deleted:    data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_SSCS_routput_processedSep-23-2021.csv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/EnsEMBL__REST_practice.html
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/RP5_102121.bai
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/RP5_102121.bam
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/abl1_sequence.txt
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/calls_il3indep1_dcs_filtered.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/chr9130835254-130887675.dnas
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.bam.gz
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.bam.gz.bai
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.sam.gz
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.sam.gz.bai
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_alignment.bai
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_alignment.bam
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_all_filtered.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered_calls.csv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered_calls.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_alignment.bai
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_alignment.bam
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_all_filtered.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_filtered.tsv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_filtered_calls.csv
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/mnv_caller_practice.Rmd
    Deleted:    data/Consensus_Data/archive/AlignmentsPractice/ranomics_december_library.csv
    Deleted:    data/Consensus_Data/archive/abl1_cds_kinasedomain.txt
    Deleted:    data/Consensus_Data/archive/abl1_genomic_coordinates.csv
    Deleted:    data/Consensus_Data/archive/abl1_genomic_coordinates.xlsx
    Deleted:    data/Consensus_Data/archive/abl1_kinasedomain_coordinates.csv
    Deleted:    data/Consensus_Data/archive/abl1_kinasedomain_coordinates.xlsx
    Deleted:    data/Consensus_Data/archive/abl_exon_positions.csv
    Deleted:    data/Consensus_Data/archive/lane11_translation.Rmd
    Deleted:    data/Consensus_Data/archive/mnv_caller_cds_aligner.Rmd
    Deleted:    data/Consensus_Data/archive/nm_005157.6_cds.txt
    Modified:   data/Consensus_Data/novogene_lane15/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane15/sample_1/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_1/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_1/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_1/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_1/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_2/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane15/sample_2/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_2/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_2/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_2/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_3/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane15/sample_3/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_3/duplex/variant_caller_outputs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/ngs/sample3a(firsthalf)/Sample3_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/ngs/variants_ann.csv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_3/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_3/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_4/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_5/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane15/sample_5/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_5/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_5/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_5/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_6/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane15/sample_6/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_6/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_6/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_6/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane15/sample_6/sscs/variant_caller_outputs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane15/sample_7/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane15/sample_7/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16a/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample11/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample12/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample13/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample14/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16a/Sample1_combined/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16a/Sample1_combined/sscs/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16a/Sample2/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16a/Sample2/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16a/Sample2/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16a/Sample6/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16a/Sample6/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample7/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample8/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16a/Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16b/Sample10/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/Sample11/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16b/Sample15/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample15/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/Sample15/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample15/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample2/duplex/duplex_sorted_filtered.tsv.gz
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    Deleted:    data/Consensus_Data/novogene_lane16b/Sample3/duplex/duplex_sorted_filtered.tsv.gz
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    Modified:   data/Consensus_Data/novogene_lane16b/Sample6/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/Sample6/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample6/sscs/sscs_sorted_filtered.tsv.gz
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    Deleted:    data/Consensus_Data/novogene_lane16b/Sample7_combined/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/Sample8_combined/.DS_Store
    Modified:   data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/duplex_sorted_filtered.tsv.gz
    New:        data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/variant_caller_outputs/variants_ann.csv
    New:        data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/variant_caller_outputs/variants_unique_ann.csv
    Modified:   data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/.DS_Store
    Deleted:    data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/variants_unique_ann.csv
    New:        data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/variants_unique_ann2.csv
    Modified:   data/Consensus_Data/novogene_lane16b/Sample9/.DS_Store
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    Deleted:    data/Consensus_Data/novogene_lane16b/Sample9/duplex/duplex_sorted_filtered.tsv.gz
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    Modified:   data/Consensus_Data/novogene_lane17/.DS_Store
    New:        data/Consensus_Data/novogene_lane17/duplex_2.fa
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    New:        data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/.DS_Store
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    Modified:   data/Consensus_Data/novogene_lane17/sample1_combined/sscs/variant_caller_outputs/variants_ann.csv
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    Deleted:    data/Consensus_Data/novogene_lane17/sample5/duplex/duplex_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane17/sample5/duplex/variant_caller_outputs/variants_ann.csv
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    New:        data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/sscs/variant_caller_outputs/variants_ann.csv
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    Modified:   data/Consensus_Data/novogene_lane17/sample6/duplex/variant_caller_outputs/variants_ann.csv
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    Modified:   data/Consensus_Data/novogene_lane17/sample6/sscs/variant_caller_outputs/variants_ann.csv
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    Deleted:    data/Consensus_Data/novogene_lane17/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Modified:   data/Consensus_Data/novogene_lane17/sample7/sscs/variant_caller_outputs/variants_ann.csv
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    Modified1:  data/Consensus_Data/Novogene_lane2/abl_ref/.DS_Store
    Modified2:  data/Consensus_Data/novogene_lane17b/.DS_Store
    Modified1:  data/Consensus_Data/Novogene_lane2/abl_ref/kraken2-master/.DS_Store
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    Modified1:  data/Consensus_Data/sscs_dcs_comparisons/.DS_Store
    Modified2:  data/Consensus_Data/novogene_lane17b/Sample2/.DS_Store
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    Modified:   data/IC50s_refseqBCRABL/Asciminib_heatmap.csv
    Modified:   data/IC50s_refseqBCRABL/Imatinib_heatmap.csv
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    New:        data/TP53data/41588_2018_204_MOESM5_ESM.csv
    New:        data/TP53data/41588_2018_204_MOESM5_ESM.xlsx
    New:        data/TP53data/readme.txt
    New:        data/TP53data/tp53_treated.pdf
    New:        data/TP53data/tp53_untreated.pdf
    Modified:   ltk_analyses.Rmd
    Modified:   output/.DS_Store
    Modified:   shinyapp/.DS_Store

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

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---

For the density plots:

library(viridisLite)
library("MASS")

Warning: package 'MASS' was built under R version 4.0.5

Attaching package: 'MASS'

The following object is masked from 'package:plotly':

    select

The following object is masked from 'package:dplyr':

    select

theme_set(theme_bw(base_size = 16))

# Get density of points in 2 dimensions.
# @param x A numeric vector.
# @param y A numeric vector.
# @param n Create a square n by n grid to compute density.
# @return The density within each square.
get_density <- function(x, y, ...) {
  dens <- MASS::kde2d(x, y, ...)
  ix <- findInterval(x, dens$x)
  iy <- findInterval(y, dens$y)
  ii <- cbind(ix, iy)
  return(dens$z[ii])
}

set.seed(1)
dat <- data.frame(
  x = c(
    rnorm(1e4, mean = 0, sd = 0.1),
    rnorm(1e3, mean = 0, sd = 0.1)
  ),
  y = c(
    rnorm(1e4, mean = 0, sd = 0.1),
    rnorm(1e3, mean = 0.1, sd = 0.2)
  )
)

This piece of code picks up some of the analysis done in ABL_unevenness_analysis.Rmd

Seeing how well our imatinib resistance mutants work with cosmic mutants

# source("code")
source("code/res_residues_adder.R")
source("code/variants_parser.R")
source("code/compare_samples.R")
source("code/resmuts_adder.R")
source("code/cosmic_data_adder.R")

data=read.csv("output/ABLEnrichmentScreens/Imatinib_Enrichment_2.20.23_v2.csv",header = T,stringsAsFactors = F)
data=read.csv("output/ABLEnrichmentScreens/Imat_Enrichment_bgmerged_2.22.23.csv",header = T,stringsAsFactors = F)
# class(data)
data=res_residues_adder(data)
data=cosmic_data_adder(data)
# data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs.x,netgr_obs.y))
data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs_screen1,netgr_obs_screen2))
data$resmut_cosmic="neither"
data[data$cosmic_present%in%TRUE,"resmut_cosmic"]="cosmic"
data[data$resmuts%in%TRUE,"resmut_cosmic"]="resmut"
data$resmut_cosmic=factor(data$resmut_cosmic,levels=c("neither","cosmic","resmut"))


ggplot(data%>%filter(protein_start>=242,protein_start<=494),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))

plotly=ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Cosmic\n Observed \n Mutant"))+scale_fill_manual(values=c("gray","orange","red"))

ggplotly(plotly)

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=score_screen1,y=score_screen2))+
  geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
  geom_abline()+
  scale_x_continuous(name="Score D0 D2")+
  scale_y_continuous(name="Score D0 D4")+
  labs(fill="Cosmic\n Mutant")+
  scale_fill_manual(values=c("gray90","orange","red"))

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean))+geom_boxplot(aes(fill=resmut_cosmic))+scale_fill_manual(values=c("gray90","orange","red"))

# a=data%>%filter(score_mean%in%c(NA,NaN))
# a=data_cosmic%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0,cosmic_present%in%T)

Netgr Plots for putting in presentation

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")

# ggsave("ImatinibEnrichment_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+
  scale_y_continuous(name="Enrichcment Score")+
  scale_x_discrete(name="Mutant")+
  scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
  theme(axis.text.x=element_text(angle=90, hjust=1),
        axis.text=element_text(size=6),
        panel.grid.major = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.background = element_blank())+
  theme(legend.position = "none")

# ggsave("ImatinibEnrichment_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)


ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
  geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
  geom_abline()+
  scale_x_continuous(name="Net Growth Rate D0 D2")+
  scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
  labs(fill="Sanger\n Mutant")+
  scale_fill_manual(values=c("gray90","orange","red"))+
  theme(legend.position = "none")

a=data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494)

# ggsave("ImatinibEnrichment_Plot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)

ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean,fill=resmut_cosmic))+
  geom_violin(color="black")+
  geom_boxplot(color="black",width=.1)+
  # geom_boxplot(color="black")+
  scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))

# ggsave("ImatinibEnrichment_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-netgr_mean),y=netgr_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))

ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
  geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
  geom_abline()+
  scale_x_continuous(name="Net Growth Rate D0 D2")+
  scale_y_continuous(name="Net Growth Rate D0 D4")+
  labs(fill="Sanger\n Mutant")+
  scale_fill_manual(values=c("gray90","orange","red"))+
  theme(legend.position = "none")

ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=score_screen1,y=score_screen2))+
  geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
  geom_abline()+
  scale_x_continuous(name="Net Growth Rate D0 D2")+
  scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
  labs(fill="Sanger\n Mutant")+
  scale_fill_manual(values=c("gray90","orange","red"))+
  theme(legend.position = "none")

Score plots for putting in presentation

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")

# ggsave("ImatinibEnrichment_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)

ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+
  scale_y_continuous(name="Enrichcment Score")+
  scale_x_discrete(name="Mutant")+
  scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
  theme(axis.text.x=element_text(angle=90, hjust=1),
        axis.text=element_text(size=6),
        panel.grid.major = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.background = element_blank())+
  theme(legend.position = "none")

# ggsave("ImatinibEnrichment_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)


ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
  geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
  geom_abline()+
  scale_x_continuous(name="Net Growth Rate D0 D2")+
  scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
  labs(fill="Sanger\n Mutant")+
  scale_fill_manual(values=c("gray90","orange","red"))+
  theme(legend.position = "none")

a=data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494)

# ggsave("ImatinibEnrichment_Plot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)

ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean,fill=resmut_cosmic))+
  geom_violin(color="black")+
  geom_boxplot(color="black",width=.1)+
  # geom_boxplot(color="black")+
  scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))

# ggsave("ImatinibEnrichment_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)

# a=data%>%filter(protein_start>=242,protein_start<=494)
# a=data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1)
# b=a[order(a$score_mean,decreasing=TRUE),]
# b=b[c(1:200),]
# c=a%>%filter(!resmut_cosmic%in%"neither")

Session information

sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] MASS_7.3-55        viridisLite_0.3.0  RColorBrewer_1.1-2 doParallel_1.0.15 
 [5] iterators_1.0.12   foreach_1.5.0      tictoc_1.0         plotly_4.9.2.1    
 [9] ggplot2_3.3.3      dplyr_1.0.6        stringr_1.4.0     

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0  xfun_0.31         bslib_0.3.1       purrr_0.3.4      
 [5] colorspace_1.4-1  vctrs_0.3.8       generics_0.0.2    htmltools_0.5.2  
 [9] yaml_2.2.1        utf8_1.1.4        rlang_0.4.11      jquerylib_0.1.4  
[13] later_1.0.0       pillar_1.6.1      glue_1.4.1        withr_2.4.2      
[17] DBI_1.1.0         lifecycle_1.0.0   munsell_0.5.0     gtable_0.3.0     
[21] workflowr_1.6.2   htmlwidgets_1.5.1 codetools_0.2-16  evaluate_0.14    
[25] labeling_0.3      knitr_1.28        fastmap_1.1.0     crosstalk_1.1.0.1
[29] httpuv_1.5.2      fansi_0.4.1       Rcpp_1.0.4.6      promises_1.1.0   
[33] backports_1.1.7   scales_1.1.1      jsonlite_1.7.2    farver_2.0.3     
[37] fs_1.4.1          digest_0.6.25     stringi_1.7.5     rprojroot_1.3-2  
[41] grid_4.0.0        tools_4.0.0       magrittr_2.0.1    sass_0.4.1       
[45] lazyeval_0.2.2    tibble_3.1.2      crayon_1.4.1      tidyr_1.1.3      
[49] pkgconfig_2.0.3   ellipsis_0.3.2    data.table_1.12.8 assertthat_0.2.1 
[53] rmarkdown_2.14    httr_1.4.2        R6_2.4.1          git2r_0.27.1     
[57] compiler_4.0.0