Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / raerose01/deconstructSigs issues and pull requests

#77 - tri.counts.method for hg38 genome

Issue - State: open - Opened by tanubrata 10 months ago

#76 - Switch df[,col] to df[[col]] to get column vectors

Pull Request - State: open - Opened by rhagenson about 1 year ago

#75 - Enable the usage of custom genome and exome in whichSignatures

Pull Request - State: open - Opened by Yunuuuu over 1 year ago - 1 comment

#74 - moving data content to sysdata?

Issue - State: open - Opened by pawelqs almost 2 years ago

#73 - whichsignatures not working

Issue - State: open - Opened by temizna over 2 years ago

#72 - Normalisation approaches for targeted panels

Issue - State: open - Opened by ARChakravarthy over 2 years ago - 1 comment

#71 - Please release v1.9.0 for automated installations

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

#70 - Update whichSignatures.R

Pull Request - State: open - Opened by ljl-suosi over 3 years ago - 2 comments

#69 - Was blacklist used to create tri.count.genome?

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

#68 - Normalization method for whole exome data

Issue - State: open - Opened by seunghun23 over 3 years ago

#67 - mut.to.sigs.input for DBS signatures creates empty output

Issue - State: open - Opened by kittysher almost 4 years ago - 5 comments

#66 - Update to Mutational Signatures (v3.1 - June 2020)

Issue - State: closed - Opened by kvaldez almost 4 years ago - 1 comment

#65 - plotSignatures do not display title

Issue - State: open - Opened by Jingjiao-ma about 4 years ago - 1 comment

#64 - normalization of hg38 exome

Issue - State: open - Opened by ChelseaCHENX about 4 years ago - 1 comment

#63 - vcf.to.sigs.input() Error arguments imply differing number of rows: 1, 0

Issue - State: open - Opened by alpreyes about 4 years ago - 4 comments

#62 - Cosine Similarity

Issue - State: open - Opened by DarioS about 4 years ago

#61 - Error With bwakit Alignments

Issue - State: open - Opened by DarioS about 4 years ago

#60 - update to COSMIC Mutational Signatures (v3 - May 2019)

Issue - State: closed - Opened by chjp about 4 years ago - 1 comment

#59 - mut.to.sigs.input for DBS

Issue - State: closed - Opened by darwinchangz over 4 years ago - 1 comment

#58 - Doubt when using updated signature matrices

Issue - State: closed - Opened by Dagsbio over 4 years ago - 1 comment

#57 - Added stacked bar chart and smart db colouring

Pull Request - State: closed - Opened by sfacista over 4 years ago - 1 comment

#56 - New COSMIC signatures (v3)

Issue - State: closed - Opened by rahulk87 over 4 years ago - 4 comments

#55 - Fix DBS input from file

Pull Request - State: closed - Opened by rbonneville over 4 years ago

#54 - Plotting the signatures gives error

Issue - State: closed - Opened by beginner984 over 4 years ago - 1 comment

#52 - "signature weights" no longer displayed in graphics

Issue - State: closed - Opened by spete021 over 4 years ago - 4 comments

#51 - Trinucleotide Counts for More Genomes

Issue - State: open - Opened by DarioS about 5 years ago

#50 - signature matrix for new Alexandrov SBS signatures?

Issue - State: closed - Opened by emham about 5 years ago - 8 comments

#48 - Unknown error with my data

Issue - State: open - Opened by beginner984 over 5 years ago

#47 - custom panel normalization

Issue - State: open - Opened by idanbudin over 5 years ago - 1 comment

#46 - Error on installation

Issue - State: closed - Opened by mozack over 5 years ago - 3 comments

#45 - Mutational Signatures for mouse mutation data?

Issue - State: open - Opened by SNRNS over 5 years ago

#44 - How to make signatures for multiple samples at once?

Issue - State: open - Opened by stevekm over 5 years ago

#43 - Filtering exome SNVs

Issue - State: open - Opened by ysbioinfo over 5 years ago

#42 - h38 support for deconstructSigs

Issue - State: closed - Opened by AdamuUu over 5 years ago - 1 comment

#41 - Error in FUN(left, right) : non-numeric argument to binary operator

Issue - State: closed - Opened by Gandalfy almost 6 years ago - 3 comments

#39 - mut.to.sigs.input out of memory error

Issue - State: closed - Opened by lpalomerol almost 6 years ago - 1 comment

#38 - mut.to.sigs.input function does not work even on sample data

Issue - State: closed - Opened by mkkuhner almost 6 years ago - 3 comments

#37 - Tri nucleoide frequency for exome data

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

#36 - Re:tri nucleotide frequency of exome and genome.

Issue - State: closed - Opened by aslam24 almost 6 years ago - 1 comment

#35 - error in converting vcf to sigs.input

Issue - State: closed - Opened by Sumithrasank about 6 years ago - 1 comment

#34 - Weighting of mutations

Issue - State: open - Opened by lima1 about 6 years ago

#33 - subscript out of bounds

Issue - State: closed - Opened by ZackDC about 6 years ago - 4 comments

#32 - Possible to save `plotSignatures` object and print later?

Issue - State: closed - Opened by stevekm about 6 years ago - 4 comments

#31 - chr name problem for GRCh38

Issue - State: open - Opened by Wszwei about 6 years ago

#30 - Using variants from chromosome X and Y

Issue - State: closed - Opened by Rashesh7 about 6 years ago

#28 - question about the tri.count.method

Issue - State: closed - Opened by MariaCartolano over 6 years ago - 1 comment

#27 - issue with BSgenome.Hsapiens.UCSC.hg38 in mut.to.sigs.input function

Issue - State: closed - Opened by Puputnik over 6 years ago - 3 comments

#26 - "Check ref bases -- not all match context" warning message

Issue - State: closed - Opened by stevekm over 6 years ago - 4 comments

#25 - Normalization method for RNA-Seq data?

Issue - State: open - Opened by stevekm over 6 years ago

#23 - Many Samples in my Maf files

Issue - State: closed - Opened by AteeqMKhaliq almost 7 years ago - 3 comments

#22 - Problem w plotSignatures and makePie

Issue - State: closed - Opened by lelawrence almost 7 years ago

#21 - SSE threshold

Issue - State: closed - Opened by Rashesh7 almost 7 years ago

#20 - Use with non-human genome

Issue - State: closed - Opened by nriddiford almost 7 years ago - 19 comments

#19 - mut.to.sigs.input Error in GrCH38

Issue - State: closed - Opened by mgala81 about 7 years ago - 4 comments

#18 - More normalization

Issue - State: open - Opened by sigven about 7 years ago

#17 - Normalisation to spesific TF context?

Issue - State: closed - Opened by mortunco about 7 years ago - 2 comments

#16 - non-default genomes

Issue - State: closed - Opened by rsiddaway about 7 years ago - 2 comments

#15 - problem with mut.to.sigs.input

Issue - State: closed - Opened by juansearch about 7 years ago - 4 comments

#14 - Update vcf.to.sigs.input.R

Pull Request - State: closed - Opened by csardas about 7 years ago

#13 - vcf.to.sigs.input() size of alt1 is empty

Issue - State: closed - Opened by csardas about 7 years ago

#12 - Whole Genome normalization question

Issue - State: closed - Opened by Rashesh7 over 7 years ago - 5 comments

#11 - The ESCA data

Issue - State: closed - Opened by Rashesh7 over 7 years ago - 1 comment

#10 - Mutation Limit

Issue - State: closed - Opened by Lab13UBIMED over 7 years ago - 2 comments

#9 - change the colors of the plotSignatures function

Issue - State: closed - Opened by alexvat over 7 years ago - 2 comments

#8 - Save plots to a file

Issue - State: closed - Opened by patidarr over 7 years ago - 2 comments

#7 - Minor bug in arbitrary bsg implementation.

Issue - State: closed - Opened by jtpoirier over 7 years ago - 2 comments

#6 - hg38 support

Issue - State: closed - Opened by LeonardJ09 over 7 years ago - 2 comments

#5 - Thank You Rachel

Issue - State: closed - Opened by blecuacp almost 8 years ago

#4 - Weights assigned to each signature do not always add up to 1

Issue - State: closed - Opened by blecuacp almost 8 years ago - 1 comment

#3 - Adding parameter 'bsg' to make code accessible to earlier genome builds

Pull Request - State: closed - Opened by emm13 almost 8 years ago - 4 comments

#2 - normalization question for whole exome sequencing data

Issue - State: closed - Opened by YingYa over 8 years ago - 13 comments

#1 - normalization question for whole genome

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