UMCUGenetics MutationalPatterns issues

UMCUGenetics / MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

MIT License

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issues

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problem with get_mut_type(data, type = "dbs", predefined_dbs_mbs = FALSE)

#87 riccardobergamin opened 7 months ago
0
count_dbs_contexts() error

#86 ThomasGro opened 9 months ago
1
Expected number of INDELs using genomic_distribution

#85 cutleraging opened 9 months ago
3
How to solve this error: The input GRanges and the ref_genome share no seqnames (chromosome names)

#84 GuidoGallo closed 9 months ago
0
easyrun error:

#83 asmo2a opened 1 year ago
1
GenomeInfoDb::seqlevelsStyle(gr) <- GenomeInfoDb::seqlevelsStyle(genome)

#82 annecarolm opened 1 year ago
1
Update README.md

#81 mroosmalen closed 1 year ago
0
Mutation matrix as input instead of vcf files

#80 tc86 opened 1 year ago
1
Error with "read_vcfs_as_granges" function

#79 shaghayeghsoudi opened 1 year ago
1
Mutational patterns on SarsCoV2 .vcf-Files

#78 Lukas67 closed 1 year ago
6
How to obtain the SNVs belong to a typical mutational signature

#77 Liyang-Zhang opened 2 years ago
2
How to use MuationalPatterns (or if I can) with Copy number signatures

#76 ipstone opened 2 years ago
2
Use extracted signature along with SBS

#75 mcdoz2010 opened 2 years ago
4
get_known_signatures Parameter Default Mismatch

#74 DarioS closed 2 years ago
1
Allow Parallel Processing Utilising BiocParallel

#73 DarioS opened 2 years ago
1
get_mut_type for indels results in empty GRangesList

#72 kristianunger closed 2 years ago
2
Single strand mutational signatures

#71 gevro closed 2 years ago
6
VCF with SNV and indels

#70 iranmdl closed 2 years ago
0
fit_to_signatures_strict: Error in if (delta <= max_delta) { : missing value where TRUE/FALSE needed

#69 lincj1994 closed 2 years ago
1
How to deal with 'Intron' and 'IGR' variants from WES data when fitting signatures?

#68 lincj1994 closed 2 years ago
1
read_vcfs_as_granges() does not work

#67 CPTPaso closed 3 years ago
5
Duplicate variants

#66 mcdoz2010 opened 3 years ago
13
Error Reading in VCF files for rheMac10

#65 Rashesh7 closed 2 years ago
2
fit_to_signatures_strict crashes, probably when initial extraction gives all weight to one signature

#64 jeff-mandell closed 2 years ago
3
mut_matrix error

#63 xiw588 closed 2 years ago
3
Cosine similarity to COSMIC DBS and Indel signatures

#62 maanmi closed 3 years ago
2
unexpected behaviour of read_vcfs_as_granges()

#61 ChristofferFlensburg closed 2 years ago
5
Order of SNV types in mutation matrix

#60 kittysher closed 3 years ago
2
How to perform the mutational pattern analyses based on maf file or tab delimited MAF file

#59 lincj1994 opened 3 years ago
1
Compatibility issues with custom forged BSgenomes

#58 joshbaskaran closed 2 years ago
2
Installation with Conda

#57 kevwilhelm95 closed 3 years ago
3
Error: There are some REF or ALT bases, that do not belong to any of the categories.

#56 pdiakumis closed 3 years ago
4
Using a new genome

#55 mullerbsf closed 2 years ago
26
Binomial test p value

#54 FrancisBlokzijl closed 2 years ago
1
Why mut_mat + 0.0001?

#53 b-niu closed 4 years ago
2
Axis lable offsets

#52 sternp closed 4 years ago
1
New release?

#51 pdiakumis closed 3 years ago
6
replication strand bias

#50 FreekManders closed 4 years ago
0
replication strand bias

#49 FreekManders closed 4 years ago
2
Error with mut_type_occurrences function.

#48 galavots closed 4 years ago
3
DBS and Indels

#47 bastiaanvdroest closed 4 years ago
3
Develop2

#46 bastiaanvdroest closed 4 years ago
1
Segfault (Memory Not Mapped) When Trying to Load Sample Data

#45 drmrgd closed 4 years ago
7
mut_mat error

#44 twoshoes closed 4 years ago
5
Data format of using this package

#43 xiw588 closed 5 years ago
6
Alternative input formats

#42 yunguan-wang closed 5 years ago
1
nmf() rank factorization step is removing data and not plotting estimate rank plot

#41 leowill01 closed 5 years ago
2
How to average mutational profile for a group of samples

#40 KCLiv closed 4 years ago
1
error in Loading required package: rtracklayer

#39 rescuz closed 5 years ago
1
test

#38 FrancisBlokzijl closed 5 years ago
0