Showing : SomaticSignatures • reset
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
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4
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1.6k
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Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
1
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7
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1.2k
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Help creating VRange object
vcf somaticSignatures Vrange
updated 5.0 years ago by ★ 1.3k • written 5.0 years ago by • 0
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739
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SomaticSignatures package: how can I get probability of certain mutation type within a signature?
somaticsignatures
5.4 years ago spr ▴ 10
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3.0k
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nmf function not working
somaticsignatures NMF
updated 5.5 years ago by • 0 • written 5.9 years ago by • 0
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5
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1.6k
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Somatic Signature only SNV supported
somaticsignatures
5.6 years ago TRASA • 0
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738
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Formal class VRanges versus Large VRanges
somaticsignatures vranges readvcfasvranges
5.7 years ago guillaume.dachy • 0
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1.1k
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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 6.2 years ago by 3.9k • written 6.2 years ago by • 0
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6
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2.8k
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Somaticsignature NMF problem
somaticsignatures NMF
updated 6.6 years ago by • 0 • written 7.3 years ago by • 0
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2
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1.6k
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Trouble while concatenating VRanges object ()
somaticsignatures somaticsignatures package readvcfasvranges vranges
6.8 years ago • updated 6.7 years ago guillaume.dachy • 0
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4
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1.8k
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SomaticSignatures: Compare my signatures with published COSMIC datasets
somaticsignatures
6.7 years ago john.alexander • 0
2
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3
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1.3k
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SomaticSignatures package : motifMatrix function trouble
somaticsignatures
6.9 years ago • updated 6.8 years ago guillaume.dachy • 0
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1
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1.0k
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plotMutationSpectrum Colour By Patient with Multiple Samples
plotMutationSpectrum somaticsignatures somaticsignatures package
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by ▴ 30
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5
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1.7k
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SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
somaticsignatures somaticsignatures package
7.1 years ago morovatunc • 0
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1
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1.1k
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Questions about SomaticSignatures packages
SomaticSignatures
updated 7.3 years ago by ★ 13k • written 7.3 years ago by • 0
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2
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1.2k
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SomaticSignature - Significant signature
somaticsignatures
7.5 years ago ksivapra • 0
0
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1
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1.4k
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How to compare SomaticSignatures package profiles with signatures listed by the Sanger Institute
somaticsignatures
updated 7.5 years ago by ★ 1.3k • written 7.5 years ago by ▴ 10
2
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4
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1.4k
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SomaticSignatures plotSamples error
somaticsignatures plotSamples
7.7 years ago ns • 0
3
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4
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3.6k
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Error while running SomaticSignatures
somaticsignatures
updated 7.8 years ago by ▴ 120 • written 7.8 years ago by • 0
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3
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1.1k
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Observing composition of somatic signatures as barcharts
somaticsignatures
7.8 years ago arsala521 ▴ 10
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2
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1.0k
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Number of tumor samples and analysis by SomaticSignature Package
somaticsignatures
updated 7.8 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
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1
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972
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Input files for somaticSignature
somaticsignatures
updated 7.8 years ago by ★ 1.3k • written 7.8 years ago by • 0
1
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2
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1.1k
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motifMatrix input object type, confused VRange and GRange
somaticsignatures
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
3
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8
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1.9k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 7.9 years ago by ★ 11k • written 7.9 years ago by • 0
3
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3
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1.4k
views
makeVRangesFromGRanges throws coercing "factor" to "NA" error
r packages somaticsignatures variantannotation
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
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3
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1.3k
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Sequence Context of Somatic Variants
somaticsignatures mutation context
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
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4
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1.8k
views
Converting VCF to VRanges
somaticsignatures vranges
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
2
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8
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1.6k
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Regarding Somatic Mutation Signature
somaticsignatures
updated 8.0 years ago by ★ 1.3k • written 8.0 years ago by ▴ 10
0
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5
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1.7k
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Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
somaticsignatures RGBL
8.0 years ago user31888 ▴ 30
0
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8
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1.7k
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Regarding somatic signature package
somaticsignatures
updated 8.0 years ago by ★ 1.3k • written 8.1 years ago by ▴ 10
2
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2
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1.0k
views
geom problem with SomaticSignatures plotRainfall
SomaticSignatures
updated 8.1 years ago by ★ 1.3k • written 8.1 years ago by ▴ 20
1
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1
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1.1k
views
Contribution of Signature in each sample
mutational signature somaticSignatures
updated 8.1 years ago by ★ 1.3k • written 8.1 years ago by • 0
0
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1
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1.2k
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Fitting somatic signatures to alexandrovs's
somaticsignatures somaticsignatures mutationcontext
updated 8.1 years ago by ★ 1.3k • written 8.1 years ago by • 0
1
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2
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1.5k
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Combining GRange/VRange objects
granges vranges readvcfasvranges somaticsignatures
updated 8.1 years ago by ★ 11k • written 8.1 years ago by • 0
1
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2
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1.3k
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SomaticSignatures - Getting Started & Trouble Shooting
software error somaticsignatures somaticsignatures mutationcontext
8.2 years ago jpluta26 • 0
0
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1
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1.5k
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mutational signatures problems
bsgenome readvcf tcga annotation somaticsignatures
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by • 0
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1
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1.2k
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specify the color in plotMutationSpectrum() of SomaticSignatures library
SomaticSignatures
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by ▴ 100
0
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6
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1.6k
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SomaticSignatures: Interpretation of plotSamples graphs
somaticsignatures
8.3 years ago • updated 8.2 years ago Jane Merlevede ▴ 90
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2
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1.1k
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SomaticSignatures: properties of the estimated signatures
somaticsignatures
8.3 years ago Jane Merlevede ▴ 90
0
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1
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1.1k
views
SomaticSignatures: extract low level information
somaticsignatures somaticsignatures mutationcontext
updated 8.4 years ago by ★ 1.3k • written 8.4 years ago by • 0
0
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1
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1.6k
views
SomaticSignatures: negative entries after ComBat adjustment
sva somaticsignatures batch effect nmf
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by • 0
0
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1
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1.5k
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Questions about SomaticSignatures package
somaticsignatures
8.8 years ago • updated 8.7 years ago Asma rabe ▴ 290
3
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4
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1.5k
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Number of Signatures
somaticsignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ▴ 290
0
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4
replies
1.3k
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Assess number of Signatures in Somatic signatures
somaticsignatures
8.8 years ago Asma rabe ▴ 290
1
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3
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1.1k
views
nReplicates in Somatic Signatures
somaticsignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ▴ 290
0
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2
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1.5k
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Number of Signatures in SomaticSignatures package
SomaticSignatures
8.8 years ago Asma rabe ▴ 290
0
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1
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1.6k
views
.maf file in SomaticSignatures
somaticsignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by • 0
2
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3
replies
1.6k
views
Determining number of signatures in SomaticSignatures
somaticsignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ▴ 30
4
votes
1
reply
1.2k
views
SomaticSignature - what samples contributed to each signature
somaticsignatures
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ▴ 30
6
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12
replies
4.2k
views
SomaticSignatures: Compare my datas with validated mutational signatures
somaticsignatures mutational signature
updated 8.8 years ago by ▴ 30 • written 9.6 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
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Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
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So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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