AlexandrovLab/SigProfilerExtractor issues and pull requests

#165 - U26

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

#164 - matplotlib version dependency updates

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

#163 - signature for each mutation in a sample

Issue - State: closed - Opened by sainadfensi over 1 year ago - 1 comment
Labels: enhancement

#162 - [Errno 2] No such file or directory: '~/.local/lib/python3.6/site-packages/sigProfilerPlotting/templates/DBS78.pkl'

Issue - State: closed - Opened by RTCarmo over 1 year ago - 7 comments

#161 - Development

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

#160 - SV signatures extraction

Issue - State: closed - Opened by Avramis over 1 year ago - 5 comments

#159 - questions about estimate_solution and results

Issue - State: closed - Opened by thisisliuyu almost 2 years ago - 1 comment

#158 - Development

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#157 - Remove parameter

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#156 - CNV Matrix causes error

Issue - State: closed - Opened by Ott-Alexander almost 2 years ago - 2 comments

#155 - Sample contribution mutational signatures

Issue - State: closed - Opened by msubirana almost 2 years ago - 1 comment

#154 - TypeError: _set_ticklabels() takes 2 positional arguments but 3 were given

Issue - State: closed - Opened by msubirana almost 2 years ago - 1 comment

#153 - About decomposing de novo signatures to COSMIC signatures

Issue - State: closed - Opened by FromSoSimple almost 2 years ago - 1 comment

#152 - Upgrade 19

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#151 - Key Error when running Sequenza segment input

Issue - State: closed - Opened by Fractal10 almost 2 years ago - 2 comments

#150 - U9

Pull Request - State: closed - Opened by mdbarnesUCSD almost 2 years ago

#149 - synchronisation with PyPI

Issue - State: closed - Opened by mvforster almost 2 years ago - 1 comment

#148 - Only Context working output is 6 and 18

Issue - State: closed - Opened by pinunQ almost 2 years ago - 1 comment

#147 - Using output from SigProfilerMatrixGenerator as input for SigProfilerExtractor

Issue - State: closed - Opened by rsg344 almost 2 years ago - 2 comments
Labels: good first issue

#146 - Using tab-delimited text file

Issue - State: closed - Opened by rsg344 almost 2 years ago

#145 - Development

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#144 - U5

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#143 - Default opportunity_genome to GRCh37 if no COSMIC genome

Pull Request - State: closed - Opened by marcos-diazg almost 2 years ago

#142 - Development

Pull Request - State: closed - Opened by mdbarnesUCSD almost 2 years ago

#141 - require current versions of sigprofiler tools

Pull Request - State: closed - Opened by mdbarnesUCSD almost 2 years ago

#140 - Upgrade #2

Pull Request - State: closed - Opened by mdbarnesUCSD almost 2 years ago

#139 - Make MutationType column name consistant

Pull Request - State: closed - Opened by mdbarnesUCSD almost 2 years ago

#138 - number of signatures

Issue - State: closed - Opened by dmusachio almost 2 years ago - 2 comments

#137 - PCG64DXSM causing run problems

Issue - State: closed - Opened by laurelhiatt almost 2 years ago - 2 comments

#136 - copy number signature extraction - try to decompose to published CNV signature

Issue - State: closed - Opened by ipstone almost 2 years ago - 1 comment

#135 - interpretation of the results

Issue - State: closed - Opened by stroke1989 almost 2 years ago - 1 comment
Labels: good first issue

#134 - updates to v1.1.8

Pull Request - State: closed - Opened by rvangara almost 2 years ago

#133 - Did you update the Extractor reference signature of CNV from the Preprint to the Nature?

Issue - State: closed - Opened by lincj1994 about 2 years ago - 1 comment

#132 - Decomposition plots are empty

Issue - State: closed - Opened by kw10 about 2 years ago - 8 comments
Labels: bug

#131 - Activity for signature is 0, but shows as 2% in decomposition plot

Issue - State: closed - Opened by oliverartz about 2 years ago - 2 comments

#130 - SigProfilerExtractor, no ID signatures, ValueError: operands could not be broadcast together with shapes (78,0) (0,0)

Issue - State: closed - Opened by oliverartz about 2 years ago - 3 comments

#129 - Error on running in cluster

Issue - State: closed - Opened by linkmonica about 2 years ago - 5 comments

#128 - DBS78A de novo signature tallied separately even though 100% COSMIC DBS4

Issue - State: closed - Opened by toddajohnson about 2 years ago - 1 comment

#127 - How can I load my specific reference genome? (Pig)

Issue - State: closed - Opened by jingydz about 2 years ago - 1 comment

#126 - Is it possible to find which mutational signature a SNV belongs to?

Issue - State: closed - Opened by lincj1994 about 2 years ago - 1 comment

#125 - custom reference signatures

Issue - State: closed - Opened by vr1087 over 2 years ago - 1 comment

#124 - Spa linking

Pull Request - State: closed - Opened by rvangara over 2 years ago

#123 - CUDA Update

Pull Request - State: closed - Opened by mdbarnesUCSD over 2 years ago - 1 comment

#122 - Running out of memory on computing cluster

Issue - State: closed - Opened by kgeyer over 2 years ago - 3 comments

#121 - RuntimeError:An attempt has been made to start a new process before the current process has finished its bootstrapping phase.

Issue - State: closed - Opened by DimitrisGrig over 2 years ago - 3 comments

#120 - How to install reference genome

Issue - State: closed - Opened by TomhitsJerry over 2 years ago - 2 comments

#119 - Ensure functions respect requested number of CPUs

Pull Request - State: closed - Opened by david-a-parry over 2 years ago

#118 - the "collapse_to_SBS96=True" not working for SBS288 and SBS1536

Issue - State: closed - Opened by YingYa over 2 years ago - 6 comments

#117 - Adding parameter newsignature_threshold to decomposition module

Pull Request - State: closed - Opened by rvangara over 2 years ago

#116 - the given project path does not appear to exist

Issue - State: closed - Opened by stroke1989 over 2 years ago - 4 comments

#115 - sigProfilerExtractor ignores some vcf files

Issue - State: closed - Opened by AnastasiaShind over 2 years ago - 2 comments

#114 - Fixing decompose module

Pull Request - State: closed - Opened by rvangara over 2 years ago

#113 - Reconstructed spectrum after signature extraction

Issue - State: closed - Opened by itsvenu over 2 years ago - 8 comments

#111 - Identifying optimum number of signatures

Issue - State: closed - Opened by MySelvan over 2 years ago - 2 comments

#92 - Plot produce with sig. mutations at 0

Issue - State: closed - Opened by natir almost 3 years ago - 12 comments

#87 - SigProfilerExtractor throwing an error with my vcf files

Issue - State: closed - Opened by Sonia-Bedi almost 3 years ago - 3 comments

#72 - Reproducibility of results

Issue - State: closed - Opened by Marozi2 about 3 years ago - 4 comments

#43 - subroutines.py line 1410 -- shutil.rmtree OSError: [Errno 16] Device or resource busy

Issue - State: closed - Opened by mlayeghi almost 4 years ago - 6 comments

GitHub / AlexandrovLab/SigProfilerExtractor issues and pull requests