ShixiangWang sigminer issues

ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

https://shixiangwang.github.io/sigminer/

Other

147 stars 19 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Caused by error in `quadprog::solve.QP()`: ! matrix D in quadratic function is not positive definite!

#467 shenhaizhongdechanrao opened 1 month ago
1
some question about function sig_tally when method ='S'

#466 shenhaizhongdechanrao closed 1 month ago
1
NULL Row Names in NMF Matrix When Using sig_tally() with Wang Method

#465 selkamand opened 2 months ago
1
Issue with read_vcf function

#464 arianlundberg closed 2 months ago
3
Request to make sig_tally output a matrix when run on single sample rearrangement datasets

#463 selkamand closed 3 months ago
2
About relative contribution and mutation counts in samples

#462 ShepherdZh closed 3 months ago
1
warning in read_maf_minimal

#461 ShixiangWang opened 4 months ago
0
StarSignDNA

#460 ShixiangWang opened 4 months ago
0
mm39 mouse gbuild

#459 karolina16 opened 4 months ago
1
Warning when running example data through sigminer rearrangement tally

#458 selkamand closed 3 months ago
2
Fragile and silent dependency on 'copynumber' in SV signature tally

#457 selkamand closed 5 months ago
2
v3 plan & roadmap

#456 ShixiangWang opened 6 months ago
1
https://www.biorxiv.org/content/10.1101/2024.05.20.594967v1

#455 ShixiangWang opened 6 months ago
0
Update fun docs

#454 ShixiangWang closed 6 months ago
0
Making sig_tally output a matrix when run with a single sample in ID / DBS / ALL mode (like SBS already does)

#453 selkamand closed 8 months ago
3
Questions about sig_fit()

#452 xiw588 closed 8 months ago
4
Please do not change future options

#451 HenrikBengtsson closed 8 months ago
1
'Matrices' returned by sig_tally are actually just vectors when only 1 sample is supplied

#450 selkamand closed 10 months ago
3
Custom color problem

#449 RuimeiL closed 11 months ago
1
Rules of CNV/SV signature selection

#448 RuimeiL closed 11 months ago
4
Support T2T genome

#447 ShixiangWang closed 11 months ago
3
for the mode "ID", error

#445 eajeong closed 11 months ago
2
Error in RS analysis

#444 RuimeiL closed 11 months ago
3
cosmic signature outdated

#442 ShixiangWang closed 11 months ago
1
Issue recording from email

#441 ShixiangWang closed 1 year ago
0
Error: package or namespace load failed for ‘sigminer’

#439 benjamhbrs closed 1 year ago
1
An error is detected in bootstrap fitting process

#438 zxwang-cloak closed 1 year ago
7
异常高的SBS39的组分

#436 wangshun1121 closed 1 year ago
12
issues of applying sig_extract

#435 xiw588 closed 1 year ago
1
Add annotations for exposure profile show_sig_exposure(mt_sig)

#433 xiw588 closed 1 year ago
16
issues when using data frame as input for get_Aneuploidy_score function

#431 WiesVallentgoed closed 1 year ago
5
support custom oppo matrix in from option of sig_convert?

#430 ShixiangWang opened 1 year ago
0
how to pick the number of signature based on the index.

#428 songeric1107 closed 1 year ago
16
update bib reference data and doc

#427 ShixiangWang closed 1 year ago
1
fix: changed hardcoded 'multisession' to `set_future_strategy` ...

#426 selkamand closed 1 year ago
1
Warning: Strategy 'multiprocess' is deprecated in future (>= 1.20.0)

#425 selkamand closed 1 year ago
0
https://www.biorxiv.org/content/10.1101/2023.02.09.527740v1.full

#424 ShixiangWang opened 1 year ago
3
Feature Request: Take a minimal data.frame as input

#423 selkamand closed 1 year ago
3
getSeq

#422 ShixiangWang closed 1 year ago
1
Row names discrepancy for latest_CN_GRCh37CNS_TCGA

#421 dnousome closed 2 years ago
2
show_cn_distribution with scale_chr = T

#420 jrcodina closed 2 years ago
4
signature and reference version problem

#419 Aimee2018 closed 2 years ago
5
idea from panel sig

#418 ShixiangWang opened 2 years ago
3
show_cn_distribution() y axis clarification

#417 rajeha closed 2 years ago
3
show_cn_freq_circos() y axis

#416 rajeha closed 2 years ago
2
get_sig_similarity only goes up to COSMIC_30

#415 maia-munteanu closed 2 years ago
2
Getting similarities for CNV signatures

#414 rajeha closed 2 years ago
6
感觉诗翔兄的创意被Nature剽窃了。。。

#413 wangshun1121 closed 2 years ago
3
update cosmic reference signature

#412 ShixiangWang closed 2 years ago
1
增加一个cn signature的文档

#411 ShixiangWang closed 2 years ago
0