Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / greenelab/pdx_exomeseq issues and pull requests

#74 - Github issues

Pull Request - State: closed - Opened by gwaybio about 6 years ago

#73 - hotfix merge conflict

Pull Request - State: closed - Opened by gwaybio about 6 years ago

#72 - Add human only plots

Pull Request - State: closed - Opened by gwaybio about 6 years ago

#71 - Human Only Pipeline

Pull Request - State: closed - Opened by gwaybio about 6 years ago

#70 - Rerunning Analysis Pipeline with Human Only Samples

Pull Request - State: closed - Opened by gwaybio about 6 years ago - 1 comment

#69 - Adding pipeline steps and logic for human only variant calling

Pull Request - State: closed - Opened by gwaybio about 6 years ago

#68 - Add ATM and RNF45 Variants to WES mutation Figure

Issue - State: closed - Opened by gwaybio over 6 years ago

#67 - Run Human Samples through Pipeline Without Disambiguation Step

Issue - State: closed - Opened by gwaybio over 6 years ago

#66 - Update Oncoprint Data Processing

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#65 - Adding Missing Sample to mosdepth plot

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#64 - Update Axis Sample Labels in Replicate Similarity Plot

Issue - State: closed - Opened by gwaybio over 6 years ago

#63 - rerun mosdepth for KS29/048-M1-F0

Issue - State: closed - Opened by gwaybio over 6 years ago

#62 - Adding Figure Summary + Legends

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#61 - Rerun Full Pipeline

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#60 - Updating README

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#59 - Rerun Oncoprint Data Generation with New Sample IDs

Pull Request - State: closed - Opened by gwaybio over 6 years ago - 1 comment

#58 - Update disambiguate plot

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#57 - Updating Filtration Summary KDE plots

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#56 - Update upset plots

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#55 - Updating Script to Filter Variants

Pull Request - State: closed - Opened by gwaybio over 6 years ago - 1 comment

#54 - Update Mosdepth Output - Adding Sorted Legend

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#53 - Compare shared mutations in 008 and 040

Issue - State: open - Opened by gwaybio over 6 years ago

#52 - Variants Correlated with Chemoresistance

Issue - State: open - Opened by gwaybio over 6 years ago

#52 - Variants Correlated with Chemoresistance

Issue - State: open - Opened by gwaybio over 6 years ago

#51 - Adding Two Columns to Phenotype DataFrame

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#50 - Rename Samples to More Intuitive Identifiers

Issue - State: closed - Opened by gwaybio over 6 years ago

#49 - Write Figure Titles and Figure Legends

Issue - State: closed - Opened by gwaybio over 6 years ago

#47 - Add OncoPrint, Similarity, and UpSetR visualizations BEFORE COSMIC filtration

Issue - State: closed - Opened by gwaybio over 6 years ago - 1 comment

#46 - Add UpSetR plots for Venn Diagrams

Issue - State: closed - Opened by gwaybio over 6 years ago

#45 - Prepare table of variants filtered with over 1000 reads

Issue - State: closed - Opened by gwaybio over 6 years ago - 1 comment

#44 - Labeled Outliers on mos-depth plot

Issue - State: closed - Opened by gwaybio over 6 years ago

#43 - Reorder Oncoprint Diagram

Issue - State: closed - Opened by gwaybio over 6 years ago

#42 - update to correct flowchart

Pull Request - State: closed - Opened by gwaybio over 6 years ago

#41 - Adding Variant Passage Flow Visualizations and Data

Pull Request - State: closed - Opened by gwaybio almost 7 years ago - 1 comment

#40 - Update Oncoprint Notebook Data + Visualization

Pull Request - State: closed - Opened by gwaybio almost 7 years ago

#39 - Trivial Pull Request - Updating Kernel for Analysis Notebooks

Pull Request - State: closed - Opened by gwaybio almost 7 years ago

#38 - Adding mouse and ambiguous percent labels to figure

Pull Request - State: closed - Opened by gwaybio almost 7 years ago

#37 - Add Analysis Environment File

Pull Request - State: closed - Opened by gwaybio almost 7 years ago - 1 comment

#36 - Visualize Merged Variants Filtration

Pull Request - State: closed - Opened by gwaybio almost 7 years ago - 2 comments

#34 - Samtools Merge of Technical Replicates

Pull Request - State: closed - Opened by gwaybio almost 7 years ago - 1 comment

#33 - Gene count summary across passages

Issue - State: closed - Opened by gwaybio almost 7 years ago - 1 comment

#32 - Redo visualizations with the concatenated final variants

Issue - State: closed - Opened by gwaybio almost 7 years ago - 2 comments

#31 - Rerun pipeline with concatenated replicates

Issue - State: closed - Opened by gwaybio almost 7 years ago

#30 - Remove files

Pull Request - State: closed - Opened by gwaybio almost 7 years ago

#29 - Hotfix readme urls

Pull Request - State: closed - Opened by gwaybio almost 7 years ago

#28 - Visualize percentages of human/mouse/ambiguous in plot

Issue - State: closed - Opened by gwaybio almost 7 years ago

#27 - Add script to summarize alignment statistics

Issue - State: closed - Opened by gwaybio almost 7 years ago - 4 comments

#26 - Call Variants in "Ambiguous" assigned reads

Issue - State: closed - Opened by gwaybio almost 7 years ago - 1 comment

#25 - Modularizing the Pipeline

Issue - State: closed - Opened by danich1 almost 7 years ago - 6 comments

#24 - Big PR merging entire project into master

Pull Request - State: closed - Opened by gwaybio almost 7 years ago - 7 comments

#23 - VennDiagram version conflict in conda environment

Issue - State: closed - Opened by gwaybio almost 7 years ago - 2 comments

#22 - Annotate Variants

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#21 - samtools rmdup failed on 23 samples

Issue - State: closed - Opened by gwaybio about 7 years ago - 2 comments

#20 - Sort Position Failed for 8 samples

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#19 - Run Disambiguate

Issue - State: closed - Opened by gwaybio about 7 years ago - 2 comments

#18 - Run MAPEX

Issue - State: closed - Opened by gwaybio about 7 years ago - 3 comments

#17 - Run GATK MuTect2

Issue - State: closed - Opened by gwaybio about 7 years ago - 5 comments

#16 - Remove duplicate reads from position sorted bam file

Issue - State: closed - Opened by gwaybio about 7 years ago

#15 - Samtools sort fixmate adjusted bam files by position

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#14 - Run samtools fixmate to clean up tags and match read pairs

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#13 - Samtools sort and bam compression failed for 5 samples

Issue - State: closed - Opened by gwaybio about 7 years ago - 2 comments

#12 - Sort data with samtools and compress to bam

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#11 - bwa mem failed for one sample

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#10 - Run BWA mem on validated samples output from TrimGalore

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#9 - Create a phenotype data matrix

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#8 - Write method that will identify and process files that failed on cluster

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment
Labels: enhancement

#7 - Update README

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#6 - Trim_Galore now accepts paired reads

Issue - State: closed - Opened by gwaybio about 7 years ago - 3 comments

#5 - Re-Index Human and Mouse Genome with updated conda BWA

Issue - State: closed - Opened by gwaybio about 7 years ago

#4 - Add mapexr to command wrapper

Issue - State: closed - Opened by gwaybio about 7 years ago - 1 comment

#3 - Rerun FastQC

Issue - State: closed - Opened by gwaybio about 7 years ago - 2 comments

#2 - Adding QC reports

Pull Request - State: closed - Opened by gwaybio over 7 years ago

#1 - Develop

Pull Request - State: closed - Opened by gwaybio over 7 years ago