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greenelab
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pdx_exomeseq
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
MIT License
21
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14
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Github issues
#74
gwaybio
closed
5 years ago
0
hotfix merge conflict
#73
gwaybio
closed
5 years ago
0
Add human only plots
#72
gwaybio
closed
5 years ago
0
Human Only Pipeline
#71
gwaybio
closed
5 years ago
0
Rerunning Analysis Pipeline with Human Only Samples
#70
gwaybio
closed
6 years ago
1
Adding pipeline steps and logic for human only variant calling
#69
gwaybio
closed
6 years ago
0
Add ATM and RNF45 Variants to WES mutation Figure
#68
gwaybio
closed
6 years ago
0
Run Human Samples through Pipeline Without Disambiguation Step
#67
gwaybio
closed
6 years ago
0
Update Oncoprint Data Processing
#66
gwaybio
closed
6 years ago
0
Adding Missing Sample to mosdepth plot
#65
gwaybio
closed
6 years ago
0
Update Axis Sample Labels in Replicate Similarity Plot
#64
gwaybio
closed
6 years ago
0
rerun mosdepth for KS29/048-M1-F0
#63
gwaybio
closed
6 years ago
0
Adding Figure Summary + Legends
#62
gwaybio
closed
6 years ago
0
Rerun Full Pipeline
#61
gwaybio
closed
6 years ago
0
Updating README
#60
gwaybio
closed
6 years ago
0
Rerun Oncoprint Data Generation with New Sample IDs
#59
gwaybio
closed
6 years ago
1
Update disambiguate plot
#58
gwaybio
closed
6 years ago
0
Updating Filtration Summary KDE plots
#57
gwaybio
closed
6 years ago
0
Update upset plots
#56
gwaybio
closed
6 years ago
0
Updating Script to Filter Variants
#55
gwaybio
closed
6 years ago
1
Update Mosdepth Output - Adding Sorted Legend
#54
gwaybio
closed
6 years ago
0
Compare shared mutations in 008 and 040
#53
gwaybio
opened
6 years ago
0
Variants Correlated with Chemoresistance
#52
gwaybio
opened
6 years ago
0
Adding Two Columns to Phenotype DataFrame
#51
gwaybio
closed
6 years ago
0
Rename Samples to More Intuitive Identifiers
#50
gwaybio
closed
6 years ago
0
Write Figure Titles and Figure Legends
#49
gwaybio
closed
6 years ago
0
Add columns in gene and variant flow passage to indicate F0 and F5 only in TRIPLICATE sets
#48
gwaybio
opened
6 years ago
0
Add OncoPrint, Similarity, and UpSetR visualizations BEFORE COSMIC filtration
#47
gwaybio
closed
6 years ago
1
Add UpSetR plots for Venn Diagrams
#46
gwaybio
closed
6 years ago
0
Prepare table of variants filtered with over 1000 reads
#45
gwaybio
closed
6 years ago
1
Labeled Outliers on mos-depth plot
#44
gwaybio
closed
6 years ago
0
Reorder Oncoprint Diagram
#43
gwaybio
closed
6 years ago
0
update to correct flowchart
#42
gwaybio
closed
6 years ago
0
Adding Variant Passage Flow Visualizations and Data
#41
gwaybio
closed
6 years ago
1
Update Oncoprint Notebook Data + Visualization
#40
gwaybio
closed
6 years ago
0
Trivial Pull Request - Updating Kernel for Analysis Notebooks
#39
gwaybio
closed
6 years ago
0
Adding mouse and ambiguous percent labels to figure
#38
gwaybio
closed
6 years ago
0
Add Analysis Environment File
#37
gwaybio
closed
6 years ago
1
Visualize Merged Variants Filtration
#36
gwaybio
closed
6 years ago
2
Add Mosdepth and samtools flagstat commands to compile final bam coverage stats
#35
gwaybio
closed
6 years ago
0
Samtools Merge of Technical Replicates
#34
gwaybio
closed
6 years ago
1
Gene count summary across passages
#33
gwaybio
closed
6 years ago
1
Redo visualizations with the concatenated final variants
#32
gwaybio
closed
6 years ago
2
Rerun pipeline with concatenated replicates
#31
gwaybio
closed
6 years ago
0
Remove files
#30
gwaybio
closed
6 years ago
0
Hotfix readme urls
#29
gwaybio
closed
6 years ago
0
Visualize percentages of human/mouse/ambiguous in plot
#28
gwaybio
closed
6 years ago
0
Add script to summarize alignment statistics
#27
gwaybio
closed
6 years ago
4
Call Variants in "Ambiguous" assigned reads
#26
gwaybio
closed
6 years ago
1
Modularizing the Pipeline
#25
danich1
closed
6 years ago
6
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