Last updated: 2020-07-03

Checks: 2 0

Knit directory: MINTIE-paper-analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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: d4fe950

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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:    .Rproj.user/
    Ignored:    analysis/cache/
    Ignored:    data/RCH_B-ALL/
    Ignored:    data/leucegene/salmon_out/
    Ignored:    data/leucegene/sample_info/KMT2A-PTD_8-2.fa.xls
    Ignored:    output/Leucegene_gene_counts.tsv
    Ignored:    packrat/lib-R/
    Ignored:    packrat/lib-ext/
    Ignored:    packrat/lib/
    Ignored:    packrat/src/

Untracked files:
    Untracked:  update_results.sh

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
html e9e4917 Marek Cmero 2020-06-24 Build site.
html 0b21347 Marek Cmero 2020-06-11 Build site.
html a166ab8 Marek Cmero 2020-05-08 Build site.
html a600688 Marek Cmero 2020-05-07 Build site.
Rmd 0fde0b8 Marek Cmero 2020-05-07 Added RCH B-ALL analysis
html 5c045b5 Marek Cmero 2020-05-07 Build site.
html 90c7fd9 Marek Cmero 2020-05-06 Build site.
Rmd ff4b1dc Marek Cmero 2020-05-06 Leucegene results
html 358aa53 Marek Cmero 2020-05-04 Build site.
html 4a5d6ae Marek Cmero 2020-05-01 Build site.
Rmd 9556ebb Marek Cmero 2020-05-01 Added leucegene normals analysis. Added expressed genes analysis to leucegene gene expression analysis.
html 784838b Marek Cmero 2020-04-30 Build site.
Rmd c4c3844 Marek Cmero 2020-04-30 Added leucegene gene expression notebook
html 14a7a7b Marek Cmero 2020-04-27 Update index
Rmd 1096df5 Marek Cmero 2020-04-24 Fixed case
html 1096df5 Marek Cmero 2020-04-24 Fixed case
html 663689c Marek Cmero 2020-04-23 Build site.
Rmd e57763b Marek Cmero 2020-04-23 Initial commit
html e57763b Marek Cmero 2020-04-23 Initial commit
Rmd 9f95a7c Marek Cmero 2020-04-15 Start workflowr project.

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

MINTIE is a Method for Inferring Novel Transcripts and Isoforms using Equivalence classes.

This site contains the code for generating the figures and analyses presented in the (upcoming) MINTIE paper.

Analyses