broadinstitute ichorCNA issues

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

GNU General Public License v3.0

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Suspected error resulting in underestimated tumour fraction

#135 abcoxyzide closed 2 months ago
1
Understand subclone fraction results

#134 jgarces02 opened 2 months ago
0
PON error

#133 gagank4911 opened 2 months ago
0
Different tumor fractions estimated with different runs for the same samples

#132 Urja25 opened 3 months ago
0
Running ichorCNA on cell free mitochondrial DNA

#131 Ons14 opened 3 months ago
0
Fix bug in correctReadCounts()

#130 abcoxyzide opened 4 months ago
0
unable to find an inherited method for function ‘seqinfo’ for signature ‘"RangedData"’

#129 heweihuang closed 4 months ago
0
Could ichorCNA be used for low-pass whole genome sequencing of gDNA？

#128 feihongloveworld opened 7 months ago
0
Plotting error

#127 IanCodes opened 9 months ago
4
ISSUES WITH LOGR INFINITE VALUE

#126 Mariamamghar1 opened 10 months ago
2
Scope of application of ichorCNA?

#125 h170607 opened 10 months ago
1
Missing bins on chr19 for hg38 but not hg19

#124 zztin opened 12 months ago
0
Missing bin on some regions

#123 npt-vinh opened 12 months ago
0
Samples with 0% Tumor, but chromosome deletions?

#122 Timster28 opened 1 year ago
0
The subclonal fraction (fraction of tumor-derived DNA that is subclonal) is 0.446 but tumor fraction is 0

#121 paulhtyang opened 1 year ago
0
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :

#120 ekushele opened 1 year ago
0
Add config option for people with color vision defficiency

#119 moldovannorbert opened 1 year ago
1
Are duplicated records in BAM file counted or not?

#118 zztin opened 1 year ago
1
Rumtime error (Error in lambdas[, , i] <- na.omit(param$lambda) : incorrect number of subscripts)

#117 yaotianran opened 1 year ago
7
Error while using a BED file

#116 mokhouja opened 1 year ago
0
Final segmentation from alternate ichorCNA solutions

#115 shahmj opened 1 year ago
1
PON- missing .rds metadata columns

#114 fmadrid2 opened 1 year ago
0
correctedDepth.txt File interval missing

#113 zhangyafeng1 opened 1 year ago
0
Failed to connect to ftp.ncbi.nlm.nih.gov

#112 paulhtyang opened 1 year ago
1
Is cutoff 0.03 suitable for cfDNA 5hmC sequencing？

#111 hxlei opened 2 years ago
0
PON - unable to find an inherited method for function ‘seqinfo’ for signature ‘"data.table"’

#110 EvoMedLab opened 2 years ago
2
map_hg38_1k.wig

#109 baimianer opened 2 years ago
2
Intuitive understanding of `txnE` and `txnStrength`

#108 ilykos opened 2 years ago
1
Panel of normals for 10kb and 50kb

#107 ilykos closed 2 years ago
0
Add chrY to chrs variable for readCounter

#106 jbhiatt opened 2 years ago
0
New version release

#105 SPPearce opened 2 years ago
3
logR and copy.number in cna.seg. files

#104 daguilarvhio opened 2 years ago
1
question about coverage computation

#103 martapaoli1991 opened 2 years ago
0
Duplicate levels error after loading GenomeInfoD using mouse reference

#102 mheskett closed 2 years ago
1
Slurping

#101 applebyn opened 2 years ago
0
Exon bed

#100 mjko1210 closed 3 years ago
0
germline analysis

#99 lmanchon opened 3 years ago
0
Error with runEM in runIchorCNA.R

#98 N-TI opened 3 years ago
3
which Alignability OR Uniqueness bigwig file should I use as the input of mapCounter?

#97 hw538 opened 3 years ago
1
correct bin size

#96 ZKai0801 opened 3 years ago
0
Loading Namespace Error

#95 shashwatsahay opened 3 years ago
1
Fix pon

#94 mjko1210 closed 3 years ago
0
Chr Y empty in plots

#93 bhavi-qub opened 3 years ago
0
What are the columns in the cna.seg file?

#92 LN908 opened 3 years ago
0
Option to turn off the chrX Normalization in createPanelOfNormals.R

#91 awchrist opened 3 years ago
0
why genomewide CNV is not so "normalized" as in reference

#90 asaki1986 opened 3 years ago
1
Getting CNV result from different solution

#89 Pitithat-pu opened 3 years ago
1
ichorCNA failing to load a file from ftp.ncbi.nlm.nih.gov

#88 ury opened 3 years ago
0
Support for nonstandard genomes / species

#87 EvoMedLab opened 3 years ago
8
Maximum number of copies observed is segmentation file is 5 (without including homozygous deletions)

#86 JasMeenDar opened 3 years ago
0