This repository has been archived by the owner on Oct 2, 2024. It is now read-only.
dNdScv analysis (1/N) #58
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add R package rstatix in dockerfile
Co-authored-by: Ryan Corbett <[email protected]>
Co-authored-by: Ryan Corbett <[email protected]>
…into achroni/explore-TMB-mut-script
Generate dndscv reference file
added 9 commits
January 24, 2024 13:57
AntoniaChroni
force-pushed
the
achroni/dNdScv-analysis
branch
from
21c9e72 to
d7ab5c4
Compare
4 tasks
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Purpose/implementation Section
What scientific question is your analysis addressing?
We will use the dNdScv R package to infer driver genes for the PBTA cohort. This analysis is part of the tumor clone inference analysis.
What was your approach?
What GitHub issue does your pull request address?
Closes #57
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
There is an issue when using the
RefCDS_human_GRCh38_GencodeV39_liftover.rda as the genome reference.Is there anything that you want to discuss further?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Results
What types of results are included (e.g., table, figure)?
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.