gavinha/TitanCNA issues and pull requests

#100 - where to find ichorCNA.R and pysam version

Issue - State: open - Opened by ryao-mdanderson over 1 year ago

#99 - environment configuration

Issue - State: open - Opened by FWYX over 1 year ago

#98 - LogR and BAF

Issue - State: open - Opened by tanasa over 1 year ago

#97 - Intuitive understanding of `txnE` and `txnStrength`

Issue - State: closed - Opened by ilykos almost 3 years ago

#96 - TITAN for mm10

Issue - State: open - Opened by bhinderb almost 3 years ago

#95 - Decide on PR's/issues and create a release for dockerization?

Issue - State: open - Opened by vortexing almost 3 years ago

#94 - countPysam script returns 0 for all counts

Issue - State: open - Opened by thek71 about 3 years ago

#93 - problem with ichorCNA in snakemake

Issue - State: closed - Opened by thek71 about 3 years ago

#92 - Show segment be filtered by region width?

Issue - State: open - Opened by qindan2008 over 3 years ago - 1 comment

#91 - Run Titan on tumor-only WGS sample

Issue - State: closed - Opened by ysbioinfo over 3 years ago - 2 comments

#90 - CNV estimation for WES data using TitanCNA

Issue - State: open - Opened by asaki1986 over 3 years ago

#89 - correctReadDepth targetedSequence fix

Pull Request - State: open - Opened by wayneliuq over 3 years ago

#88 - plotIdiogram issues - SNPchip R package installation fails

Issue - State: open - Opened by dsampath31 almost 4 years ago - 3 comments

#87 - Error in as(chrDF, "RangedData") :

Issue - State: closed - Opened by LiQingsolab almost 4 years ago - 1 comment

#86 - An issue related to chrX when running ichorCNA.snakefile thru TitanCNA

Issue - State: open - Opened by wenching over 4 years ago - 1 comment

#85 - Corrected NEUT call, which seems to be a region of DLOH instead.

Issue - State: open - Opened by sahilseth over 4 years ago - 1 comment

#84 - Modify ichorCNA.snakefile for Panel of Normal (PoN)

Issue - State: closed - Opened by wjaratlerdsiri over 4 years ago - 1 comment

#83 - TitanCNA on targeted sequencing data

Issue - State: closed - Opened by neethav almost 5 years ago - 1 comment

#82 - Made cp recursive.

Pull Request - State: closed - Opened by annahoge almost 5 years ago

#81 - Patch 1

Pull Request - State: closed - Opened by annahoge about 5 years ago

#80 - Snakemake workflow query

Issue - State: open - Opened by GeorgetteTanner about 5 years ago - 1 comment

#79 - Bioconductor build error

Issue - State: closed - Opened by lima1 about 5 years ago

#78 - ichorCNA can't find packages

Issue - State: closed - Opened by fjgassner about 5 years ago - 1 comment

#77 - Non-human chromosome length

Issue - State: open - Opened by peterpdu about 5 years ago - 1 comment

#76 - setGenomeStyle mingles the number of rows of the CN data if it contains alt contigs

Issue - State: closed - Opened by lbeltrame about 5 years ago - 2 comments

#75 - Ratios shifted upwards in CN segment plot

Issue - State: open - Opened by lbeltrame over 5 years ago - 5 comments

#74 - Add SNPchip as a dependency.

Pull Request - State: closed - Opened by roryk over 5 years ago - 4 comments

#73 - selectSolution.R does not work if samples have similar names

Pull Request - State: closed - Opened by d-henness over 5 years ago

#72 - Snakemake workflow makes Titan assume male gender regardless of how config.yaml file is configured.

Issue - State: open - Opened by d-henness over 5 years ago - 2 comments
Labels: enhancement

#71 - About Chromosome Y

Issue - State: open - Opened by guanghaoli over 5 years ago - 2 comments

#70 - Cancer cell fraction

Issue - State: open - Opened by fpbarthel over 5 years ago - 2 comments

#69 - Empty optimalClusterSolution.txt

Issue - State: open - Opened by d88020 over 5 years ago - 4 comments

#68 - Several fixes for snakefile and config

Pull Request - State: open - Opened by ZhaoxiangSimonCai almost 6 years ago

#67 - Should Corrected_Ratio be NA in the .segs files?

Issue - State: closed - Opened by aleighbrown almost 6 years ago - 1 comment

#66 - Adding a small script in the snakemake scripts to parse a standard data csv into the samples.yaml format required by the snakemake pipeline

Pull Request - State: closed - Opened by aleighbrown almost 6 years ago - 1 comment

#65 - Typo in the snakemake file

Issue - State: closed - Opened by aleighbrown almost 6 years ago - 1 comment

#64 - Normal_contamination_estimate

Issue - State: open - Opened by udp3f almost 6 years ago - 11 comments

#63 - Correct allelic copy number results

Issue - State: closed - Opened by gavinha almost 6 years ago
Labels: enhancement

#62 - http://compbio.bccrc.ca/software/hmmcopy/ in readme redirects to https://shahlab.ca/

Issue - State: closed - Opened by setgree almost 6 years ago

#61 - Optimize parameters to reduce overestimation of genome doubling

Issue - State: open - Opened by gavinha almost 6 years ago - 1 comment
Labels: enhancement

#60 - Titan reporting very short CNVs

Issue - State: open - Opened by d-henness almost 6 years ago - 1 comment

#59 - No results, no exception thrown with failed ichorCNA snakemake

Issue - State: closed - Opened by MUppal almost 6 years ago - 1 comment

#58 - Multi-sample TITAN

Issue - State: closed - Opened by fpbarthel almost 6 years ago - 2 comments

#57 - Corrected_Copy_Number vs Copy_Number

Issue - State: closed - Opened by aleighbrown almost 6 years ago - 3 comments

#56 - homozygous deletion (CDKN2A) being classified as HLAMP

Issue - State: closed - Opened by fpbarthel almost 6 years ago - 1 comment

#54 - 1-based coordinates in segment output

Issue - State: closed - Opened by fpbarthel almost 6 years ago

#53 - titanCNA.R excluding chromosome X for males by default despite correction

Issue - State: closed - Opened by fpbarthel almost 6 years ago - 2 comments

#52 - A small bug in selectSolution.R

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

#51 - Check for NAs during parameter estimation

Pull Request - State: closed - Opened by chapmanb almost 6 years ago

#50 - Segmentation results missing expected gene

Issue - State: closed - Opened by aleighbrown almost 6 years ago - 5 comments

#49 - Snakemake ChildIOExcpetion

Issue - State: closed - Opened by aleighbrown almost 6 years ago - 1 comment

#48 - Parameters in TitanCNA snakemake pipeline

Issue - State: closed - Opened by ysbioinfo almost 6 years ago - 2 comments

#47 - Can Titan deal with WES data?

Issue - State: closed - Opened by ysbioinfo almost 6 years ago - 3 comments

#46 - selectSolution not selecting the best solution

Issue - State: open - Opened by fpbarthel almost 6 years ago - 11 comments

#45 - hg38 plots: data frame fix for cytoband

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

#44 - TitanCNA error if --libdir is omitted

Issue - State: closed - Opened by fpbarthel about 6 years ago

#43 - computeSDbwIndex correct?

Issue - State: closed - Opened by alashkov83 about 6 years ago - 12 comments

#42 - Plotting fix for multiple arguments

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

#41 - object 'genes' not found on hg19 test runs

Issue - State: closed - Opened by chapmanb about 6 years ago - 1 comment

#40 - Fix plotIdiogram cytoband error with build 37 runs

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

#39 - Error in cytoband[, "chrom"] : incorrect number of dimensions

Issue - State: closed - Opened by AAlhendi1707 about 6 years ago - 4 comments

#38 - Using GATK CNV with TITAN

Issue - State: open - Opened by fpbarthel about 6 years ago - 14 comments

#37 - hg38: non-internet access and plot function export

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

#36 - cytobandFile error

Issue - State: closed - Opened by elifirem about 6 years ago - 2 comments

#35 - Snakemake scripts not compatible with UCSC chromosome naming

Issue - State: closed - Opened by przemekl about 6 years ago