AlexandrovLab/SigProfilerAssignment issues and pull requests

#151 - Pdfwriter fix

Pull Request - State: closed - Opened by mdbarnesUCSD 18 days ago

#150 - Max vcf file size?

Issue - State: closed - Opened by oksalau about 1 month ago - 1 comment

#149 - Insufficient GRCh38 reference set in ID/CNV/SV of COSMIC

Issue - State: closed - Opened by shengxindaniu about 1 month ago - 2 comments

#148 - Extract mutations assigned to each SBS signature

Issue - State: closed - Opened by itigupta2429 about 1 month ago - 5 comments

#147 - median mutation burden per COSMIC signature

Issue - State: closed - Opened by eltonjrv about 2 months ago - 4 comments

#146 - Problems of uploading segmentation file

Issue - State: closed - Opened by xiw588 about 2 months ago - 6 comments

#145 - Error while providing path to installed TSB files

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

#143 - some question about exome=true

Issue - State: closed - Opened by shenhaizhongdechanrao 2 months ago - 1 comment

#142 - file used to plot following plot

Issue - State: closed - Opened by wangzunq 2 months ago - 1 comment

#141 - shapes (96,86) and (85,) not aligned: 86 (dim 1) != 85 (dim 0)

Issue - State: closed - Opened by wangzunq 3 months ago - 9 comments

#140 - Decompose fit

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

#139 - Add Docker Container

Pull Request - State: closed - Opened by mdbarnesUCSD 3 months ago

#138 - Keyboard Interrupts Ignored

Issue - State: closed - Opened by DarioS 4 months ago - 1 comment

#137 - [Question] Difference between denovo_fit and cosmic_fit

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

#136 - Is there a way to run SigProfilerAssignment on the Experimental Mutational Signatures?

Issue - State: closed - Opened by alexanderchang1 5 months ago - 1 comment

#135 - cant run through a set of samples

Issue - State: closed - Opened by LawrenceH622 5 months ago - 12 comments

#134 - Unclear Scope

Issue - State: closed - Opened by DarioS 5 months ago - 5 comments

#133 - mouse mutational signatures

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

#132 - error related to SigProfilerAssignment requires pandas==1.5.3

Issue - State: closed - Opened by allaway 5 months ago - 5 comments

#131 - Development

Pull Request - State: closed - Opened by mdbarnesUCSD 5 months ago - 1 comment

#130 - SigProfilerAssignment for targeted panels?

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

#129 - replace PyPDF2 by pypdf

Pull Request - State: closed - Opened by FelixMoelder 6 months ago - 2 comments

#128 - incompatibility with conda when importing pyPDF2

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

#127 - please rerun by setting the flag "collapse_to_SBS96 = False "

Issue - State: closed - Opened by YingYa 6 months ago - 1 comment
Labels: bug

#126 - How to generate DBS and ID report?

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

#125 - U67

Pull Request - State: closed - Opened by mdbarnesUCSD 6 months ago

#124 - Updates links

Pull Request - State: closed - Opened by mdbarnesUCSD 7 months ago

#123 - v0.1.5: Add text for stability and mutation count to the de novo signature plots

Pull Request - State: closed - Opened by mdbarnesUCSD 7 months ago

#122 - SBS signatures with numbers above 96

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

#121 - UnboundLocalError: cannot access local variable 'samples' where it is not associated with a value

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

#120 - SBS96_Decomposition_Plots.pdf is empty

Issue - State: closed - Opened by odoveestrella 8 months ago - 1 comment
Labels: enhancement

#119 - Exome renormalization seems to miss mutations

Issue - State: closed - Opened by pushpa-itagi 9 months ago - 4 comments

#118 - Tracking SBS probability for individual mutation?

Issue - State: closed - Opened by Kdreval 9 months ago - 2 comments

#117 - U57

Pull Request - State: closed - Opened by MousumyCSE 9 months ago

#116 - Error: "The context-96 decomposition plots pages were not able to be generated."

Issue - State: closed - Opened by thebrownlife 9 months ago - 4 comments

#115 - v0.1.3: Modify how ndarrays are processed

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

#114 - v0.1.2: Spa_r_i1

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

#113 - Add reindex function

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

#112 - Explanation of "context" parameter

Issue - State: closed - Opened by marcus-r-kelly 10 months ago - 3 comments

#111 - Python Version Issue

Issue - State: closed - Opened by hpoisner 10 months ago - 2 comments

#110 - I108

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

#109 - Signature decomposition error - negative values

Issue - State: closed - Opened by maia-munteanu 10 months ago - 4 comments

#108 - SV Support Update

Issue - State: closed - Opened by mdbarnesUCSD 11 months ago

#107 - Connection timed out while downloading the ref genome to install.

Issue - State: closed - Opened by AngelGarciaDeLaTorreGarcia 12 months ago - 3 comments

#106 - Cosmic v3.4

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

#105 - Possible to provide path to existing reference genome data?

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

#104 - a qusetion

Issue - State: closed - Opened by shenhaizhongdechanrao about 1 year ago - 3 comments

#103 - Question regarding exclude_signature_subgroups option

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

#102 - How do I get CN signature?

Issue - State: closed - Opened by pyuna about 1 year ago - 6 comments

#101 - I99

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

#100 - Sample data to run?

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

#99 - Unable to decompose signatures into COSMIC for SBS192 or SBS384

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

#98 - export_probabilities_per_mutation=True doesn't work with exome=True

Issue - State: closed - Opened by ImNotaGit about 1 year ago - 5 comments

#97 - Update README.md

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

#96 - Add citation to README

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

#95 - Upgrade to v0.0.32

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

#94 - Sample reconstruction plotting fails when using matrix input

Issue - State: closed - Opened by alvinwt about 1 year ago - 3 comments

#93 - Difference in Activities from SigProfilerExtractor and SigProfilerAssignment

Issue - State: closed - Opened by micoli98 over 1 year ago - 3 comments

#92 - Parameter collapse_to_SBS96

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

#91 - I77

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

#90 - Some problems with CNsig

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

#89 - I77

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

#88 - I77

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

#87 - issue running sigprofilerassignment in GEL container

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

#86 - Difference between the pan-cancer cnv signatures provided by the paper and those provided in the github data

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

#85 - Error after updating: cosmic_fit() got an unexpected keyword argument 'input_type'

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

#84 - Difference between CNV signature from SigProfilerAssignment and SigprofilerExtractor

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

#83 - Local reference genome

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

#82 - Resolve issue with sample reconstruction plots and pandas version

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

#81 - SBS96 signature assignment reproducibility using SigProfilerAssignment?

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

#80 - Development

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

#79 - U49

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

#78 - Problem encountered when running the code in containers

Issue - State: closed - Opened by superjw almost 2 years ago - 4 comments
Labels: enhancement

#77 - Export probabilities Per Mutation is not working

Issue - State: closed - Opened by pushpa-itagi almost 2 years ago

#76 - Update setup.py

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

#75 - U23

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

#74 - U45

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

#73 - Up1b

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

#72 - Decompose fit: causes an error `ValueError: cannot convert float NaN to integer`

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

#71 - Decompose_fit outputs entirely different signatures

Issue - State: closed - Opened by maia-munteanu almost 2 years ago - 6 comments

#70 - Could not run ID signatures

Issue - State: closed - Opened by MeteorLiu96 almost 2 years ago - 1 comment

#69 - U1b

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

#68 - Unable to decompose de novo copy number signatures

Issue - State: closed - Opened by aliahhawari almost 2 years ago - 5 comments

#67 - Development

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

#66 - Update README SV and CN input types

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

#65 - v0.0.23: Fix ID decomp plots and add ID tests

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

#64 - Development

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

#63 - Update README.md

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

#62 - need help for the flag "signatures"

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