gavinha TitanCNA issues

gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

GNU General Public License v3.0

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issues

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where to find ichorCNA.R and pysam version

#100 ryao-mdanderson opened 1 year ago
0
environment configuration

#99 FWYX opened 1 year ago
0
LogR and BAF

#98 tanasa opened 1 year ago
0
Intuitive understanding of `txnE` and `txnStrength`

#97 ilykos closed 2 years ago
0
TITAN for mm10

#96 bhinderb opened 2 years ago
0
Decide on PR's/issues and create a release for dockerization?

#95 vortexing opened 2 years ago
0
countPysam script returns 0 for all counts

#94 thek71 opened 3 years ago
0
problem with ichorCNA in snakemake

#93 thek71 closed 3 years ago
0
Show segment be filtered by region width?

#92 qindan2008 opened 3 years ago
1
Run Titan on tumor-only WGS sample

#91 ysbioinfo closed 2 years ago
2
CNV estimation for WES data using TitanCNA

#90 asaki1986 opened 3 years ago
0
correctReadDepth targetedSequence fix

#89 wayneliuq opened 3 years ago
0
plotIdiogram issues - SNPchip R package installation fails

#88 dsampath31 opened 3 years ago
3
Error in as(chrDF, "RangedData") :

#87 LiQingsolab closed 3 years ago
1
An issue related to chrX when running ichorCNA.snakefile thru TitanCNA

#86 wenching opened 4 years ago
1
Corrected NEUT call, which seems to be a region of DLOH instead.

#85 sahilseth opened 4 years ago
1
Modify ichorCNA.snakefile for Panel of Normal (PoN)

#84 wjaratlerdsiri closed 4 years ago
1
TitanCNA on targeted sequencing data

#83 neethav closed 4 years ago
1
Made cp recursive.

#82 annahoge closed 4 years ago
0
Patch 1

#81 annahoge closed 5 years ago
0
Snakemake workflow query

#80 GeorgetteTanner opened 5 years ago
1
Bioconductor build error

#79 lima1 closed 5 years ago
0
ichorCNA can't find packages

#78 fjgassner closed 5 years ago
1
Non-human chromosome length

#77 peterpdu opened 5 years ago
1
setGenomeStyle mingles the number of rows of the CN data if it contains alt contigs

#76 lbeltrame closed 4 years ago
2
Ratios shifted upwards in CN segment plot

#75 lbeltrame opened 5 years ago
5
Add SNPchip as a dependency.

#74 roryk closed 5 years ago
4
selectSolution.R does not work if samples have similar names

#73 d-henness closed 5 years ago
0
Snakemake workflow makes Titan assume male gender regardless of how config.yaml file is configured.

#72 d-henness opened 5 years ago
2
About Chromosome Y

#71 guanghaoli opened 5 years ago
2
Cancer cell fraction

#70 fpbarthel opened 5 years ago
2
Empty optimalClusterSolution.txt

#69 d88020 opened 5 years ago
4
Several fixes for snakefile and config

#68 ZhaoxiangSimonCai opened 5 years ago
0
Should Corrected_Ratio be NA in the .segs files?

#67 aleighbrown closed 5 years ago
1
Adding a small script in the snakemake scripts to parse a standard data csv into the samples.yaml format required by the snakemake pipeline

#66 aleighbrown closed 5 years ago
1
Typo in the snakemake file

#65 aleighbrown closed 5 years ago
1
Normal_contamination_estimate

#64 udp3f opened 5 years ago
11
Correct allelic copy number results

#63 gavinha closed 5 years ago
0
http://compbio.bccrc.ca/software/hmmcopy/ in readme redirects to https://shahlab.ca/

#62 setgree closed 5 years ago
0
Optimize parameters to reduce overestimation of genome doubling

#61 gavinha opened 5 years ago
1
Titan reporting very short CNVs

#60 d-henness opened 5 years ago
1
No results, no exception thrown with failed ichorCNA snakemake

#59 MUppal closed 5 years ago
1
Multi-sample TITAN

#58 fpbarthel closed 5 years ago
2
Corrected_Copy_Number vs Copy_Number

#57 aleighbrown closed 5 years ago
3
homozygous deletion (CDKN2A) being classified as HLAMP

#56 fpbarthel closed 5 years ago
1
1-based coordinates in segment output

#54 fpbarthel closed 5 years ago
0
titanCNA.R excluding chromosome X for males by default despite correction

#53 fpbarthel closed 5 years ago
2
A small bug in selectSolution.R

#52 ysbioinfo closed 5 years ago
6
Check for NAs during parameter estimation

#51 chapmanb closed 5 years ago
0
Segmentation results missing expected gene

#50 aleighbrown closed 5 years ago
5