issues
search
greenelab
/
pdx_exomeseq
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
MIT License
21
stars
14
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Github issues
#74
gwaybio
closed
6 years ago
0
hotfix merge conflict
#73
gwaybio
closed
6 years ago
0
Add human only plots
#72
gwaybio
closed
6 years ago
0
Human Only Pipeline
#71
gwaybio
closed
6 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
Next