gavinha / TitanCNA

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

gavinha/TitanCNA Issues

An issue related to chrX when running ichorCNA.snakefile thru TitanCNA
Updated 10 months ago1
where to find ichorCNA.R and pysam version
Updated a year ago
environment configuration
Updated a year ago
LogR and BAF
Updated a year ago
Show segment be filtered by region width?
Updated 2 years ago1
Run Titan on tumor-only WGS sample
Closed 2 years ago2
Intuitive understanding of `txnE` and `txnStrength`
Closed 3 years ago
TITAN for mm10
Updated 3 years ago
Decide on PR's/issues and create a release for dockerization?
Updated 3 years ago
countPysam script returns 0 for all counts
Updated 3 years ago
problem with ichorCNA in snakemake
Closed 3 years ago
Empty optimalClusterSolution.txt
Updated 3 years ago4
CNV estimation for WES data using TitanCNA
Updated 3 years ago
plotIdiogram issues - SNPchip R package installation fails
Updated 4 years ago3
Error in as(chrDF, "RangedData") :
Closed 4 years ago1
Normal_contamination_estimate
Updated 4 years ago11
Modify ichorCNA.snakefile for Panel of Normal (PoN)
Closed 4 years ago1
TitanCNA on targeted sequencing data
Closed 4 years ago1
Corrected NEUT call, which seems to be a region of DLOH instead.
Updated 4 years ago1
selectSolution not selecting the best solution
Updated 5 years ago11
setGenomeStyle mingles the number of rows of the CN data if it contains alt contigs
Closed 5 years ago2
Non-human chromosome length
Updated 5 years ago1
Snakemake workflow query
Updated 5 years ago1
Bioconductor build error
Closed 5 years ago
ichorCNA can't find packages
Closed 5 years ago1
Ratios shifted upwards in CN segment plot
Updated 5 years ago5
A small bug in selectSolution.R
Closed 5 years ago6
Parameters in TitanCNA snakemake pipeline
Closed 5 years ago2
Snakemake workflow makes Titan assume male gender regardless of how config.yaml file is configured.
Updated 5 years ago2
Correct allelic copy number results
Closed 5 years ago
Cancer cell fraction
Updated 5 years ago2
About Chromosome Y
Updated 5 years ago2
Optimize parameters to reduce overestimation of genome doubling
Updated 6 years ago1
Should Corrected_Ratio be NA in the .segs files?
Closed 6 years ago1
Snakemake ChildIOExcpetion
Closed 6 years ago1
computeSDbwIndex correct?
Closed 6 years ago12
Typo in the snakemake file
Closed 6 years ago1
No results, no exception thrown with failed ichorCNA snakemake
Closed 6 years ago1
Can Titan deal with WES data?
Closed 6 years ago3
http://compbio.bccrc.ca/software/hmmcopy/ in readme redirects to https://shahlab.ca/
Closed 6 years ago
Multi-sample TITAN
Closed 6 years ago2
Titan reporting very short CNVs
Updated 6 years ago1
titanCNA.R excluding chromosome X for males by default despite correction
Closed 6 years ago2
Segmentation results missing expected gene
Closed 6 years ago5
Corrected_Copy_Number vs Copy_Number
Closed 6 years ago3
homozygous deletion (CDKN2A) being classified as HLAMP
Closed 6 years ago1
1-based coordinates in segment output
Closed 6 years ago
TitanCNA error if --libdir is omitted
Closed 6 years ago
object 'genes' not found on hg19 test runs
Closed 6 years ago1
Error in cytoband[, "chrom"] : incorrect number of dimensions
Closed 6 years ago4