Last updated: 2024-04-05

Checks: 2 0

Knit directory: GibbsDTE-code/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: bebf946

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 bebf946. 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: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rprofile
    Ignored:    .Rproj.user/
    Ignored:    .gitattributes
    Ignored:    .gitignore
    Ignored:    GibbsDTE-code.Rproj
    Ignored:    code/lung/data/slurm-10678225.out
    Ignored:    code/lung/index-subread/.RData
    Ignored:    code/lung/index-subread/buildindex.Rout
    Ignored:    code/lung/index-subread/slurm-15397947.out
    Ignored:    code/lung/index-subread/slurm-15397948.out
    Ignored:    code/lung/index-subread/slurm-15397949.out
    Ignored:    code/lung/index/slurm-10679764.out
    Ignored:    code/lung/index/slurm-10679768.out
    Ignored:    code/lung/index/slurm-10684814.out
    Ignored:    code/lung/kallisto/slurm-16121443.out
    Ignored:    code/lung/salmon/.RData
    Ignored:    code/lung/salmon/runWasabi.Rout
    Ignored:    code/lung/salmon/slurm-15257704.out
    Ignored:    code/lung/salmon/slurm-15397973.out
    Ignored:    code/lung/salmon/slurm-15887027.out
    Ignored:    code/lung/subread/.nextflow.log
    Ignored:    code/lung/subread/.nextflow/
    Ignored:    code/lung/subread/log/
    Ignored:    code/lung/subread/report.html
    Ignored:    code/lung/subread/slurm-15398003.out
    Ignored:    code/lung/subread/timeline.html
    Ignored:    code/lung/subread/trace-20240201-45121600.txt
    Ignored:    code/pkg/.Rbuildignore
    Ignored:    code/pkg/.Rhistory
    Ignored:    code/pkg/.Rproj.user/
    Ignored:    code/pkg/pkg.Rproj
    Ignored:    code/pkg/src/.gitignore
    Ignored:    code/pkg/src/RcppExports.o
    Ignored:    code/pkg/src/pkg.so
    Ignored:    code/pkg/src/rcpparma_hello_world.o
    Ignored:    code/simulation/.RData
    Ignored:    code/simulation/slurm-15466798.out
    Ignored:    code/simulation/slurm-15466799_1.out
    Ignored:    code/simulation/slurm-15466799_10.out
    Ignored:    code/simulation/slurm-15466799_100.out
    Ignored:    code/simulation/slurm-15466799_101.out
    Ignored:    code/simulation/slurm-15466799_102.out
    Ignored:    code/simulation/slurm-15466799_103.out
    Ignored:    code/simulation/slurm-15466799_104.out
    Ignored:    code/simulation/slurm-15466799_105.out
    Ignored:    code/simulation/slurm-15466799_106.out
    Ignored:    code/simulation/slurm-15466799_107.out
    Ignored:    code/simulation/slurm-15466799_108.out
    Ignored:    code/simulation/slurm-15466799_109.out
    Ignored:    code/simulation/slurm-15466799_11.out
    Ignored:    code/simulation/slurm-15466799_110.out
    Ignored:    code/simulation/slurm-15466799_111.out
    Ignored:    code/simulation/slurm-15466799_112.out
    Ignored:    code/simulation/slurm-15466799_113.out
    Ignored:    code/simulation/slurm-15466799_114.out
    Ignored:    code/simulation/slurm-15466799_115.out
    Ignored:    code/simulation/slurm-15466799_116.out
    Ignored:    code/simulation/slurm-15466799_117.out
    Ignored:    code/simulation/slurm-15466799_118.out
    Ignored:    code/simulation/slurm-15466799_119.out
    Ignored:    code/simulation/slurm-15466799_12.out
    Ignored:    code/simulation/slurm-15466799_120.out
    Ignored:    code/simulation/slurm-15466799_121.out
    Ignored:    code/simulation/slurm-15466799_122.out
    Ignored:    code/simulation/slurm-15466799_123.out
    Ignored:    code/simulation/slurm-15466799_124.out
    Ignored:    code/simulation/slurm-15466799_125.out
    Ignored:    code/simulation/slurm-15466799_126.out
    Ignored:    code/simulation/slurm-15466799_127.out
    Ignored:    code/simulation/slurm-15466799_128.out
    Ignored:    code/simulation/slurm-15466799_129.out
    Ignored:    code/simulation/slurm-15466799_13.out
    Ignored:    code/simulation/slurm-15466799_130.out
    Ignored:    code/simulation/slurm-15466799_131.out
    Ignored:    code/simulation/slurm-15466799_132.out
    Ignored:    code/simulation/slurm-15466799_133.out
    Ignored:    code/simulation/slurm-15466799_134.out
    Ignored:    code/simulation/slurm-15466799_135.out
    Ignored:    code/simulation/slurm-15466799_136.out
    Ignored:    code/simulation/slurm-15466799_137.out
    Ignored:    code/simulation/slurm-15466799_138.out
    Ignored:    code/simulation/slurm-15466799_139.out
    Ignored:    code/simulation/slurm-15466799_14.out
    Ignored:    code/simulation/slurm-15466799_140.out
    Ignored:    code/simulation/slurm-15466799_141.out
    Ignored:    code/simulation/slurm-15466799_142.out
    Ignored:    code/simulation/slurm-15466799_143.out
    Ignored:    code/simulation/slurm-15466799_144.out
    Ignored:    code/simulation/slurm-15466799_145.out
    Ignored:    code/simulation/slurm-15466799_146.out
    Ignored:    code/simulation/slurm-15466799_147.out
    Ignored:    code/simulation/slurm-15466799_148.out
    Ignored:    code/simulation/slurm-15466799_149.out
    Ignored:    code/simulation/slurm-15466799_15.out
    Ignored:    code/simulation/slurm-15466799_150.out
    Ignored:    code/simulation/slurm-15466799_151.out
    Ignored:    code/simulation/slurm-15466799_152.out
    Ignored:    code/simulation/slurm-15466799_153.out
    Ignored:    code/simulation/slurm-15466799_154.out
    Ignored:    code/simulation/slurm-15466799_155.out
    Ignored:    code/simulation/slurm-15466799_156.out
    Ignored:    code/simulation/slurm-15466799_157.out
    Ignored:    code/simulation/slurm-15466799_158.out
    Ignored:    code/simulation/slurm-15466799_159.out
    Ignored:    code/simulation/slurm-15466799_16.out
    Ignored:    code/simulation/slurm-15466799_160.out
    Ignored:    code/simulation/slurm-15466799_161.out
    Ignored:    code/simulation/slurm-15466799_162.out
    Ignored:    code/simulation/slurm-15466799_163.out
    Ignored:    code/simulation/slurm-15466799_164.out
    Ignored:    code/simulation/slurm-15466799_165.out
    Ignored:    code/simulation/slurm-15466799_166.out
    Ignored:    code/simulation/slurm-15466799_167.out
    Ignored:    code/simulation/slurm-15466799_168.out
    Ignored:    code/simulation/slurm-15466799_169.out
    Ignored:    code/simulation/slurm-15466799_17.out
    Ignored:    code/simulation/slurm-15466799_170.out
    Ignored:    code/simulation/slurm-15466799_171.out
    Ignored:    code/simulation/slurm-15466799_172.out
    Ignored:    code/simulation/slurm-15466799_173.out
    Ignored:    code/simulation/slurm-15466799_174.out
    Ignored:    code/simulation/slurm-15466799_175.out
    Ignored:    code/simulation/slurm-15466799_176.out
    Ignored:    code/simulation/slurm-15466799_177.out
    Ignored:    code/simulation/slurm-15466799_178.out
    Ignored:    code/simulation/slurm-15466799_179.out
    Ignored:    code/simulation/slurm-15466799_18.out
    Ignored:    code/simulation/slurm-15466799_180.out
    Ignored:    code/simulation/slurm-15466799_181.out
    Ignored:    code/simulation/slurm-15466799_182.out
    Ignored:    code/simulation/slurm-15466799_183.out
    Ignored:    code/simulation/slurm-15466799_184.out
    Ignored:    code/simulation/slurm-15466799_185.out
    Ignored:    code/simulation/slurm-15466799_186.out
    Ignored:    code/simulation/slurm-15466799_187.out
    Ignored:    code/simulation/slurm-15466799_188.out
    Ignored:    code/simulation/slurm-15466799_189.out
    Ignored:    code/simulation/slurm-15466799_19.out
    Ignored:    code/simulation/slurm-15466799_190.out
    Ignored:    code/simulation/slurm-15466799_191.out
    Ignored:    code/simulation/slurm-15466799_192.out
    Ignored:    code/simulation/slurm-15466799_193.out
    Ignored:    code/simulation/slurm-15466799_194.out
    Ignored:    code/simulation/slurm-15466799_195.out
    Ignored:    code/simulation/slurm-15466799_196.out
    Ignored:    code/simulation/slurm-15466799_197.out
    Ignored:    code/simulation/slurm-15466799_198.out
    Ignored:    code/simulation/slurm-15466799_199.out
    Ignored:    code/simulation/slurm-15466799_2.out
    Ignored:    code/simulation/slurm-15466799_20.out
    Ignored:    code/simulation/slurm-15466799_200.out
    Ignored:    code/simulation/slurm-15466799_21.out
    Ignored:    code/simulation/slurm-15466799_22.out
    Ignored:    code/simulation/slurm-15466799_23.out
    Ignored:    code/simulation/slurm-15466799_24.out
    Ignored:    code/simulation/slurm-15466799_25.out
    Ignored:    code/simulation/slurm-15466799_26.out
    Ignored:    code/simulation/slurm-15466799_27.out
    Ignored:    code/simulation/slurm-15466799_28.out
    Ignored:    code/simulation/slurm-15466799_29.out
    Ignored:    code/simulation/slurm-15466799_3.out
    Ignored:    code/simulation/slurm-15466799_30.out
    Ignored:    code/simulation/slurm-15466799_31.out
    Ignored:    code/simulation/slurm-15466799_32.out
    Ignored:    code/simulation/slurm-15466799_33.out
    Ignored:    code/simulation/slurm-15466799_34.out
    Ignored:    code/simulation/slurm-15466799_35.out
    Ignored:    code/simulation/slurm-15466799_36.out
    Ignored:    code/simulation/slurm-15466799_37.out
    Ignored:    code/simulation/slurm-15466799_38.out
    Ignored:    code/simulation/slurm-15466799_39.out
    Ignored:    code/simulation/slurm-15466799_4.out
    Ignored:    code/simulation/slurm-15466799_40.out
    Ignored:    code/simulation/slurm-15466799_41.out
    Ignored:    code/simulation/slurm-15466799_42.out
    Ignored:    code/simulation/slurm-15466799_43.out
    Ignored:    code/simulation/slurm-15466799_44.out
    Ignored:    code/simulation/slurm-15466799_45.out
    Ignored:    code/simulation/slurm-15466799_46.out
    Ignored:    code/simulation/slurm-15466799_47.out
    Ignored:    code/simulation/slurm-15466799_48.out
    Ignored:    code/simulation/slurm-15466799_49.out
    Ignored:    code/simulation/slurm-15466799_5.out
    Ignored:    code/simulation/slurm-15466799_50.out
    Ignored:    code/simulation/slurm-15466799_51.out
    Ignored:    code/simulation/slurm-15466799_52.out
    Ignored:    code/simulation/slurm-15466799_53.out
    Ignored:    code/simulation/slurm-15466799_54.out
    Ignored:    code/simulation/slurm-15466799_55.out
    Ignored:    code/simulation/slurm-15466799_56.out
    Ignored:    code/simulation/slurm-15466799_57.out
    Ignored:    code/simulation/slurm-15466799_58.out
    Ignored:    code/simulation/slurm-15466799_59.out
    Ignored:    code/simulation/slurm-15466799_6.out
    Ignored:    code/simulation/slurm-15466799_60.out
    Ignored:    code/simulation/slurm-15466799_61.out
    Ignored:    code/simulation/slurm-15466799_62.out
    Ignored:    code/simulation/slurm-15466799_63.out
    Ignored:    code/simulation/slurm-15466799_64.out
    Ignored:    code/simulation/slurm-15466799_65.out
    Ignored:    code/simulation/slurm-15466799_66.out
    Ignored:    code/simulation/slurm-15466799_67.out
    Ignored:    code/simulation/slurm-15466799_68.out
    Ignored:    code/simulation/slurm-15466799_69.out
    Ignored:    code/simulation/slurm-15466799_7.out
    Ignored:    code/simulation/slurm-15466799_70.out
    Ignored:    code/simulation/slurm-15466799_71.out
    Ignored:    code/simulation/slurm-15466799_72.out
    Ignored:    code/simulation/slurm-15466799_73.out
    Ignored:    code/simulation/slurm-15466799_74.out
    Ignored:    code/simulation/slurm-15466799_75.out
    Ignored:    code/simulation/slurm-15466799_76.out
    Ignored:    code/simulation/slurm-15466799_77.out
    Ignored:    code/simulation/slurm-15466799_78.out
    Ignored:    code/simulation/slurm-15466799_79.out
    Ignored:    code/simulation/slurm-15466799_8.out
    Ignored:    code/simulation/slurm-15466799_80.out
    Ignored:    code/simulation/slurm-15466799_81.out
    Ignored:    code/simulation/slurm-15466799_82.out
    Ignored:    code/simulation/slurm-15466799_83.out
    Ignored:    code/simulation/slurm-15466799_84.out
    Ignored:    code/simulation/slurm-15466799_85.out
    Ignored:    code/simulation/slurm-15466799_86.out
    Ignored:    code/simulation/slurm-15466799_87.out
    Ignored:    code/simulation/slurm-15466799_88.out
    Ignored:    code/simulation/slurm-15466799_89.out
    Ignored:    code/simulation/slurm-15466799_9.out
    Ignored:    code/simulation/slurm-15466799_90.out
    Ignored:    code/simulation/slurm-15466799_91.out
    Ignored:    code/simulation/slurm-15466799_92.out
    Ignored:    code/simulation/slurm-15466799_93.out
    Ignored:    code/simulation/slurm-15466799_94.out
    Ignored:    code/simulation/slurm-15466799_95.out
    Ignored:    code/simulation/slurm-15466799_96.out
    Ignored:    code/simulation/slurm-15466799_97.out
    Ignored:    code/simulation/slurm-15466799_98.out
    Ignored:    code/simulation/slurm-15466799_99.out
    Ignored:    code/simulation/slurm-15478249_201.out
    Ignored:    code/simulation/slurm-15478249_202.out
    Ignored:    code/simulation/slurm-15478249_203.out
    Ignored:    code/simulation/slurm-15478249_204.out
    Ignored:    code/simulation/slurm-15478249_205.out
    Ignored:    code/simulation/slurm-15478249_206.out
    Ignored:    code/simulation/slurm-15478249_207.out
    Ignored:    code/simulation/slurm-15478249_208.out
    Ignored:    code/simulation/slurm-15478249_209.out
    Ignored:    code/simulation/slurm-15478249_210.out
    Ignored:    code/simulation/slurm-15478249_211.out
    Ignored:    code/simulation/slurm-15478249_212.out
    Ignored:    code/simulation/slurm-15478249_213.out
    Ignored:    code/simulation/slurm-15478249_214.out
    Ignored:    code/simulation/slurm-15478249_215.out
    Ignored:    code/simulation/slurm-15478249_216.out
    Ignored:    code/simulation/slurm-15478249_217.out
    Ignored:    code/simulation/slurm-15478249_218.out
    Ignored:    code/simulation/slurm-15478249_219.out
    Ignored:    code/simulation/slurm-15478249_220.out
    Ignored:    code/simulation/slurm-15478249_221.out
    Ignored:    code/simulation/slurm-15478249_222.out
    Ignored:    code/simulation/slurm-15478249_223.out
    Ignored:    code/simulation/slurm-15478249_224.out
    Ignored:    code/simulation/slurm-15478249_225.out
    Ignored:    code/simulation/slurm-15478249_226.out
    Ignored:    code/simulation/slurm-15478249_227.out
    Ignored:    code/simulation/slurm-15478249_228.out
    Ignored:    code/simulation/slurm-15478249_229.out
    Ignored:    code/simulation/slurm-15478249_230.out
    Ignored:    code/simulation/slurm-15478249_231.out
    Ignored:    code/simulation/slurm-15478249_232.out
    Ignored:    code/simulation/slurm-15478249_233.out
    Ignored:    code/simulation/slurm-15478249_234.out
    Ignored:    code/simulation/slurm-15478249_235.out
    Ignored:    code/simulation/slurm-15478249_236.out
    Ignored:    code/simulation/slurm-15478249_237.out
    Ignored:    code/simulation/slurm-15478249_238.out
    Ignored:    code/simulation/slurm-15478249_239.out
    Ignored:    code/simulation/slurm-15478249_240.out
    Ignored:    code/simulation/slurm-15530400.out
    Ignored:    code/simulation/summarize.Rout
    Ignored:    data/annotation/hg38/gencode.v33.annotation.gtf.gz
    Ignored:    data/annotation/mm39/
    Ignored:    data/lung-ont/220928_dge.rds
    Ignored:    data/lung/fastq/
    Ignored:    data/lung/index-kallisto/
    Ignored:    data/lung/index-subread/
    Ignored:    data/lung/index/
    Ignored:    ignore/
    Ignored:    misc/
    Ignored:    output/lung/
    Ignored:    output/simulation/

Unstaged changes:
    Modified:   analysis/lung.Rmd

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.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd cf0de1c Pedro Baldoni 2024-04-05 Changing page theme and updating frontpage
Rmd d000389 Pedro Baldoni 2023-12-11 Starting workflowr directory

This website hosts code for the Gibbs DTE pipeline paper, which presents an optimized differential transcript expression (DTE) pipeline using the latest version of the R/Bioconductor package edgeR and the Gibbs sampling algorithm from Salmon.

The presented pipeline builds upon the latest developments of edgeR 4.0, which include a new bias-corrected quasi-likelihood (QL) method with adjusted deviances for small counts, and the efficient Gibbs sampling algorithm from Salmon. A review paper from edgeR 4.0 has been preprinted by Chen et al.. The new pipeline is faster, more powerful, and provides better control of false discoveries.

Simulation study

The pages below present the necessary steps to rerun our simulation study and the code used to generate the figures and tables from the main and supplementary texts of the transcript-level differential expression paper.

Case study

The pages below present the data pre-processing steps and analysis report of the RNA-seq experiments from the human cancer cell lines H1975 and HCC827 (GEO accession GSE172421).