etal cnvkit issues - Githubissues

etal / cnvkit

Copy number variant detection from targeted DNA sequencing

http://cnvkit.readthedocs.org

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Can I use output of featurecounts output to replace the input of import-rna?

#627 deb0612 closed 3 years ago
3
CN from log2 is inaccurate at times

#626 ashbig closed 3 years ago
3
Support for vertical heatmap and various plotting refactor

#625 tetedange13 closed 3 years ago
8
segment hmm / hmm-tumor / hmm-germline method error

#624 TuanTrain closed 3 years ago
2
Experimental support for GISTIC export

#623 tetedange13 closed 3 years ago
6
How to export gistic markers?

#622 BioComSoftware closed 3 years ago
7
Difference of log2 values between .cnr file and .bintest

#621 Fponelle closed 2 years ago
8
ValueError in coverage subcommand

#620 tea-kostic opened 3 years ago
9
Error building docker image

#619 tea-kostic closed 3 years ago
4
Improve documentation for read_auto()

#618 BJWiley233 closed 2 years ago
4
Scatter plot seems to have noise

#617 jeongmeani opened 3 years ago
6
Improve documentation on `cnvkit call` and the use of VCFs

#616 tskir opened 3 years ago
0
Disable snapping to avoid losing short segments in PNG output

#615 tskir closed 3 years ago
0
Fix NetworkX transitive dependency problem in Python 3.9

#614 tskir closed 3 years ago
1
Fix median-size file selection

#613 tskir closed 3 years ago
0
midsize_file Function Does Not Return Median File

#611 michaelsykes closed 3 years ago
1
Heatmap borders per sample

#610 Aikaterini-Chatzipli closed 3 years ago
3
How do I get LOH regions from cnv kit output?

#609 smk5g5 opened 3 years ago
1
Allow specifying output filenames in autobin

#608 tskir closed 3 years ago
0
autobin command doesn't include output parameter

#607 enes-ak closed 3 years ago
1
Bump networkx dependency to 2.5

#606 auberginekenobi closed 3 years ago
1
unable to locate output file from scatter when running via Docker

#605 aadamk closed 3 years ago
2
Get unequal plot with same input

#604 jimmy200340 closed 3 years ago
3
Update the region regex to allow NCBI-style chromosome names

#603 tskir closed 3 years ago
0
unable to 'scatter' plot region of chromosome name with punctuation marks

#602 amora197 opened 3 years ago
8
negative BAF values estimating LOH

#601 john-alexander opened 3 years ago
10
Modify width/height for output figure generated from scatter command

#600 asaki1986 closed 3 years ago
2
[SUGGESTION] Add an "issue template"

#599 tetedange13 opened 3 years ago
0
Fix coverage calculation using counts

#598 tskir closed 3 years ago
3
Purity-adjusted output from genemetrics

#597 apmills opened 3 years ago
2
CNVkit import-rna Error

#596 starz77 opened 3 years ago
2
the default bin size of batch --method wgs

#595 deb0612 opened 3 years ago
3
smooth.CNA() failure

#594 ashleyacevedo opened 3 years ago
5
Coverage error

#593 joys8998 closed 3 years ago
5
Large CNV region called from WES data

#592 shhhiying opened 3 years ago
3
Missing access hg38 bed file

#591 ashwini06 opened 3 years ago
5
Fix smoothing bug when signal is shorter than a window

#590 tskir closed 3 years ago
5
Suggestion: joblib=0.17.0

#589 sssimonyang closed 1 year ago
4
fix guess_bait

#588 sssimonyang closed 3 years ago
1
[CNVkit v0.9.8] Errored smoothing with HAAR-segmentation ?

#587 tetedange13 closed 3 years ago
2
Rename `n_bins` to `probes` in genemetrics output

#586 tskir closed 3 years ago
2
cnvkit export vcf does not work when nbins is used instead of probes in cns header

#585 eriktoo closed 3 years ago
4
Clarification on parameters for calling

#584 vymao opened 3 years ago
2
Error traceback python

#583 Bettariccardo opened 3 years ago
4
cnvkit.py batch - no .cns file

#582 manolis2023 closed 3 years ago
9
Fix uniqueness check in intersect.by_shared_chroms()

#581 tskir closed 3 years ago
1
Fix subgary indexing in cnary.by_gene()

#580 tskir closed 3 years ago
2
Why some of my diagram figs have extra genes in chr1?

#579 HYan-lei closed 3 years ago
7
Error in library("DNAcopy") : there is no package called \xe2\x80\x98DNAcopy\xe2\x80\x99\nExecution halted\n'

#578 Asfetaw opened 3 years ago
2
genemetrics does not output statistics

#577 eriktoo opened 3 years ago
1

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