Ecosyste.ms: Issues

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GitHub / AlexandrovLab/SigProfilerExtractor issues and pull requests

#248 - user defined H_initials and W_initials

Issue - State: closed - Opened by MariaCartolano about 2 months ago - 2 comments

#247 - Decomposing De Novo Signatures

Issue - State: closed - Opened by ywhnet 2 months ago - 2 comments

#246 - Changelog

Issue - State: open - Opened by IanVermes 2 months ago - 1 comment

#245 - U65

Pull Request - State: closed - Opened by mdbarnesUCSD 2 months ago

#244 - CPU usage and GPU usage too little

Issue - State: closed - Opened by xiaoyaojianghuzai 2 months ago - 14 comments

#242 - index error may be caused by non-standard fields or variant type

Issue - State: closed - Opened by xiaoyaojianghuzai 3 months ago - 1 comment

#241 - "Cannot reindex on an axis with duplicate labels"-Error

Issue - State: closed - Opened by MolPath-Bioinfo 3 months ago - 1 comment

#240 - AttributeError: 'NoneType' object has no attribute 'keys'

Issue - State: closed - Opened by jennyp76 3 months ago - 3 comments

#237 - sigProfilerExtractor for ID(INDELS)

Issue - State: closed - Opened by shanimalik86 4 months ago - 5 comments

#236 - New issue with Indels

Issue - State: closed - Opened by gafishbein 4 months ago - 7 comments

#234 - Denovo Signature and Assigning Signature Matching Error

Issue - State: closed - Opened by KANGseungseok 5 months ago - 1 comment

#234 - Denovo Signature and Assigning Signature Matching Error

Issue - State: closed - Opened by KANGseungseok 5 months ago - 1 comment

#233 - Singularity container creation

Issue - State: open - Opened by Katerina10-cloud 5 months ago - 5 comments

#232 - question about the SigProfilerExtractor

Issue - State: closed - Opened by nan5895 5 months ago - 1 comment

#231 - Sample filtering before extraction

Issue - State: closed - Opened by thisisliuyu 6 months ago - 1 comment

#229 - Issue with install

Issue - State: closed - Opened by cutleraging 7 months ago - 2 comments

#228 - Infinite loop

Issue - State: closed - Opened by SukanyaPanja 7 months ago - 1 comment

#226 - COSMIC V3.4 Update

Pull Request - State: closed - Opened by mdbarnesUCSD 8 months ago

#225 - Custom opportunities matrix

Issue - State: closed - Opened by gevro 8 months ago - 8 comments

#224 - Minimum number of mutations or genome length.

Issue - State: closed - Opened by shenhaizhongdechanrao 8 months ago - 1 comment

#223 - error because of new pandas version

Issue - State: closed - Opened by sainadfensi 8 months ago - 1 comment

#222 - Strategies to improve cosine similarity per sample

Issue - State: closed - Opened by sainadfensi 9 months ago - 1 comment

#222 - Strategies to improve cosine similarity per sample

Issue - State: closed - Opened by sainadfensi 9 months ago - 1 comment

#221 - SBS384 extraction problem

Issue - State: closed - Opened by frvirard 9 months ago - 5 comments

#220 - interpretation for SBS 96D

Issue - State: closed - Opened by sainadfensi 9 months ago - 5 comments

#219 - Inquiry Regarding sigProfilerExtractor Resource Requirements

Issue - State: closed - Opened by ShinXeno 9 months ago - 1 comment

#218 - I4608

Pull Request - State: closed - Opened by mdbarnesUCSD 10 months ago

#216 - calculate cosine similarity

Issue - State: closed - Opened by me-nobody 11 months ago - 1 comment

#215 - Cosine similarity for each COSMIC signature

Issue - State: closed - Opened by nash5202 11 months ago - 1 comment

#215 - Cosine similarity for each COSMIC signature

Issue - State: open - Opened by nash5202 11 months ago

#214 - [Errno 2] No such file or directory

Issue - State: closed - Opened by KANGseungseok almost 1 year ago - 3 comments

#214 - [Errno 2] No such file or directory

Issue - State: closed - Opened by KANGseungseok almost 1 year ago - 3 comments

#214 - [Errno 2] No such file or directory

Issue - State: closed - Opened by KANGseungseok almost 1 year ago - 3 comments

#214 - [Errno 2] No such file or directory

Issue - State: closed - Opened by KANGseungseok almost 1 year ago - 3 comments

#213 - install own copy of genome

Issue - State: closed - Opened by me-nobody about 1 year ago - 1 comment

#213 - install own copy of genome

Issue - State: closed - Opened by me-nobody about 1 year ago - 1 comment

#213 - install own copy of genome

Issue - State: closed - Opened by me-nobody about 1 year ago - 1 comment

#213 - install own copy of genome

Issue - State: closed - Opened by me-nobody about 1 year ago - 1 comment

#212 - Alexandrov FTP server not responding

Issue - State: closed - Opened by daanhazelaar about 1 year ago

#212 - Alexandrov FTP server not responding

Issue - State: closed - Opened by daanhazelaar about 1 year ago

#212 - Alexandrov FTP server not responding

Issue - State: closed - Opened by daanhazelaar about 1 year ago

#212 - Alexandrov FTP server not responding

Issue - State: closed - Opened by daanhazelaar about 1 year ago

#210 - number of signatures in solution

Issue - State: closed - Opened by bakeronit about 1 year ago - 2 comments

#209 - When running VCFs, ValueError: Error: More than 30% of mutations were skipped.

Issue - State: closed - Opened by kevlumbus about 1 year ago - 2 comments

#208 - possible to change minimum signatures?

Issue - State: closed - Opened by kerstinth about 1 year ago - 2 comments

#207 - OSError: [Errno 30] Read-only file system

Issue - State: closed - Opened by maia-munteanu about 1 year ago - 1 comment

#206 - New Multi-dimensional indexing error

Issue - State: closed - Opened by kgeyer about 1 year ago - 2 comments
Labels: enhancement

#205 - ValueError on matrix containing no mutation

Issue - State: closed - Opened by Izzvoli about 1 year ago - 1 comment

#204 - Enable redirection of output files

Issue - State: closed - Opened by RubenRam over 1 year ago - 1 comment

#203 - GPU-enabled run failed

Issue - State: closed - Opened by haochenz96 over 1 year ago - 4 comments

#202 - TypeError in SigProfiler Extractor in concat

Issue - State: closed - Opened by pushpa-itagi over 1 year ago - 1 comment

#201 - Plot fix

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#200 - Some errors and question

Issue - State: closed - Opened by yoonicon over 1 year ago - 2 comments

#199 - Run SigProfilerExtractor without a reference

Issue - State: closed - Opened by gamabunta313 over 1 year ago - 1 comment

#198 - mm39 reference genome?

Issue - State: closed - Opened by conormcguinness9016 over 1 year ago - 1 comment

#197 - Bacterial genomes?

Issue - State: closed - Opened by cyrusmallon over 1 year ago - 2 comments

#196 - Usage of SigProfilerExtractor with non mutation data

Issue - State: closed - Opened by andreyurch over 1 year ago - 1 comment

#195 - Bug in 96 plot tri-nucleotide context naming?

Issue - State: closed - Opened by jlevatic over 1 year ago - 1 comment

#193 - De novo extracted signatures reconstruction seems off

Issue - State: closed - Opened by skeitaa over 1 year ago - 2 comments

#192 - CNV test

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#190 - Upgrade to v1.1.19

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#189 - Traceback

Issue - State: closed - Opened by ruinw over 1 year ago - 1 comment

#188 - v1.1.18: ID Decomposition Plot Fix and ID test

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago - 1 comment

#187 - FileNotFoundError: [Errno 2] No such file or directory:

Issue - State: closed - Opened by JLiandbear over 1 year ago - 1 comment

#186 - Dbs tests

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago - 1 comment

#185 - genInstall problem

Issue - State: closed - Opened by Glies2 over 1 year ago - 1 comment

#184 - Runtime Error: freeze_support() and dependency issues?

Issue - State: closed - Opened by roseisgold over 1 year ago - 2 comments

#182 - Generating plots for COSMIC_v3.3_DBS_GRCh37 now...

Issue - State: closed - Opened by JLiandbear over 1 year ago - 1 comment

#181 - error in plotDBS

Issue - State: closed - Opened by JLiandbear over 1 year ago - 2 comments

#179 - docker update

Issue - State: closed - Opened by snashraf over 1 year ago - 1 comment

#178 - Development

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#177 - flag make_decomposition_plots not passed on to SPA

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#174 - Tests

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#173 - Crash when trying to create Signature Plot file

Issue - State: closed - Opened by mattiyeh over 1 year ago - 2 comments

#172 - remove decomposition plots from SPE

Pull Request - State: closed - Opened by mdbarnesUCSD over 1 year ago

#171 - Differences in de novo and decomposed solution

Issue - State: closed - Opened by pushpa-itagi over 1 year ago - 1 comment

#169 - /lib64/libc.so.6: version `GLIBC_2.14' not found

Issue - State: closed - Opened by JLiandbear over 1 year ago - 1 comment

#168 - Alter COSMIC version

Issue - State: closed - Opened by RTCarmo over 1 year ago - 2 comments

#167 - CNV48 Matrix Input

Issue - State: closed - Opened by mdbarnesUCSD over 1 year ago - 1 comment

#166 - Problem with COSMIC Decomposition

Issue - State: closed - Opened by amootta over 1 year ago - 3 comments