Showing : somaticsignatures • reset
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
14 months ago vasily.dobrovolsky • 0
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4
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2.1k
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Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
1
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7
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1.5k
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Help creating VRange object
vcf somaticSignatures Vrange
updated 5.7 years ago by ★ 1.3k • written 5.7 years ago by • 0
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SomaticSignatures package: how can I get probability of certain mutation type within a signature?
somaticsignatures
6.1 years ago spr ▴ 10
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7
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3.5k
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nmf function not working
somaticsignatures NMF
updated 6.2 years ago by • 0 • written 6.5 years ago by • 0
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5
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1.9k
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Somatic Signature only SNV supported
somaticsignatures
6.3 years ago TRASA • 0
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0
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901
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Formal class VRanges versus Large VRanges
somaticsignatures vranges readvcfasvranges
6.4 years ago guillaume.dachy • 0
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1
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1.2k
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SomaticSignatures for Bioconductor 3.6 (R 3.4.3) depends on NMF, which is not available for R 3.4.3
NMF somaticsignatures R 3.4.3
updated 6.9 years ago by 4.1k • written 6.9 years ago by • 0
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6
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3.4k
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Somaticsignature NMF problem
somaticsignatures NMF
updated 7.3 years ago by • 0 • written 8.0 years ago by • 0
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2
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2.0k
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Trouble while concatenating VRanges object ()
somaticsignatures somaticsignatures package readvcfasvranges vranges
7.5 years ago • updated 7.4 years ago guillaume.dachy • 0
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4
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2.1k
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SomaticSignatures: Compare my signatures with published COSMIC datasets
somaticsignatures
7.4 years ago john.alexander • 0
2
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3
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1.5k
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SomaticSignatures package : motifMatrix function trouble
somaticsignatures
7.6 years ago • updated 7.5 years ago guillaume.dachy • 0
0
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1
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1.2k
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plotMutationSpectrum Colour By Patient with Multiple Samples
plotMutationSpectrum somaticsignatures somaticsignatures package
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by ▴ 30
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5
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2.0k
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SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
somaticsignatures somaticsignatures package
7.8 years ago morovatunc • 0
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1
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1.2k
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Questions about SomaticSignatures packages
SomaticSignatures
updated 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
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2
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1.3k
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SomaticSignature - Significant signature
somaticsignatures
8.2 years ago ksivapra • 0
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1
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1.6k
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How to compare SomaticSignatures package profiles with signatures listed by the Sanger Institute
somaticsignatures
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by ▴ 10
2
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4
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1.6k
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SomaticSignatures plotSamples error
somaticsignatures plotSamples
8.4 years ago ns • 0
3
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4
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4.0k
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Error while running SomaticSignatures
somaticsignatures
updated 8.5 years ago by ▴ 120 • written 8.5 years ago by • 0
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3
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1.3k
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Observing composition of somatic signatures as barcharts
somaticsignatures
8.5 years ago arsala521 ▴ 10
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2
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1.2k
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Number of tumor samples and analysis by SomaticSignature Package
somaticsignatures
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
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1
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1.1k
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Input files for somaticSignature
somaticsignatures
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by • 0
1
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2
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1.3k
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motifMatrix input object type, confused VRange and GRange
somaticsignatures
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 10
3
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8
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2.3k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 8.6 years ago by ★ 11k • written 8.6 years ago by • 0
3
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3
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1.5k
views
makeVRangesFromGRanges throws coercing "factor" to "NA" error
r packages somaticsignatures variantannotation
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
0
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3
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1.5k
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Sequence Context of Somatic Variants
somaticsignatures mutation context
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 10
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4
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2.1k
views
Converting VCF to VRanges
somaticsignatures vranges
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 10
2
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8
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2.0k
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Regarding Somatic Mutation Signature
somaticsignatures
updated 8.7 years ago by ★ 1.3k • written 8.7 years ago by ▴ 10
0
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5
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2.0k
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Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
somaticsignatures RGBL
8.7 years ago user31888 ▴ 30
0
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8
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2.1k
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Regarding somatic signature package
somaticsignatures
updated 8.7 years ago by ★ 1.3k • written 8.7 years ago by ▴ 10
2
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2
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1.2k
views
geom problem with SomaticSignatures plotRainfall
SomaticSignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ▴ 20
1
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1
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1.2k
views
Contribution of Signature in each sample
mutational signature somaticSignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by • 0
0
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1
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1.4k
views
Fitting somatic signatures to alexandrovs's
somaticsignatures somaticsignatures mutationcontext
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by • 0
1
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2
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1.7k
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Combining GRange/VRange objects
granges vranges readvcfasvranges somaticsignatures
updated 8.8 years ago by ★ 11k • written 8.8 years ago by • 0
1
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2
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1.5k
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SomaticSignatures - Getting Started & Trouble Shooting
software error somaticsignatures somaticsignatures mutationcontext
8.9 years ago jpluta26 • 0
0
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2
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1.8k
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mutational signatures problems
bsgenome readvcf tcga annotation somaticsignatures
updated 4 months ago by • 0 • written 8.9 years ago by • 0
0
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1
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1.3k
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specify the color in plotMutationSpectrum() of SomaticSignatures library
SomaticSignatures
updated 8.9 years ago by ★ 1.3k • written 8.9 years ago by ▴ 100
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6
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1.9k
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SomaticSignatures: Interpretation of plotSamples graphs
somaticsignatures
9.0 years ago • updated 8.9 years ago Jane Merlevede ▴ 90
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2
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1.3k
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SomaticSignatures: properties of the estimated signatures
somaticsignatures
9.0 years ago Jane Merlevede ▴ 90
0
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1
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1.3k
views
SomaticSignatures: extract low level information
somaticsignatures somaticsignatures mutationcontext
updated 9.1 years ago by ★ 1.3k • written 9.1 years ago by • 0
0
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1
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1.9k
views
SomaticSignatures: negative entries after ComBat adjustment
sva somaticsignatures batch effect nmf
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by • 0
0
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1
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1.7k
views
Questions about SomaticSignatures package
somaticsignatures
9.4 years ago Asma rabe ▴ 290
3
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4
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1.8k
views
Number of Signatures
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 290
0
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4
replies
1.5k
views
Assess number of Signatures in Somatic signatures
somaticsignatures
9.5 years ago Asma rabe ▴ 290
1
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3
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1.3k
views
nReplicates in Somatic Signatures
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 290
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2
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1.7k
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Number of Signatures in SomaticSignatures package
SomaticSignatures
9.5 years ago Asma rabe ▴ 290
0
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1
reply
1.8k
views
.maf file in SomaticSignatures
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by • 0
2
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3
replies
1.8k
views
Determining number of signatures in SomaticSignatures
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 30
4
votes
1
reply
1.4k
views
SomaticSignature - what samples contributed to each signature
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 30
6
votes
12
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4.6k
views
SomaticSignatures: Compare my datas with validated mutational signatures
somaticsignatures mutational signature
updated 9.5 years ago by ▴ 30 • written 10.3 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
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Answer: DESeq2- merging technical vs biological replicates
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