Showing : somaticSignatures • reset
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
13 months ago vasily.dobrovolsky • 0
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4
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2.0k
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Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.5 years ago by 67k • written 3.5 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 5.6 years ago by ★ 1.3k • written 5.6 years ago by • 0
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0
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908
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SomaticSignatures package: how can I get probability of certain mutation type within a signature?
somaticsignatures
6.0 years ago spr ▴ 10
0
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7
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3.5k
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nmf function not working
somaticsignatures NMF
updated 6.1 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
6.2 years ago TRASA • 0
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0
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882
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Formal class VRanges versus Large VRanges
somaticsignatures vranges readvcfasvranges
6.3 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 6.8 years ago by 4.1k • written 6.8 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 7.2 years ago by • 0 • written 7.9 years ago by • 0
1
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2
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1.9k
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Trouble while concatenating VRanges object ()
somaticsignatures somaticsignatures package readvcfasvranges vranges
7.4 years ago • updated 7.3 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
7.3 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
7.5 years ago • updated 7.4 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 7.5 years ago by ★ 1.3k • written 7.5 years ago by ▴ 30
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5
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1.9k
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SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
somaticsignatures somaticsignatures package
7.7 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 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
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2
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1.3k
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SomaticSignature - Significant signature
somaticsignatures
8.1 years ago ksivapra • 0
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 8.1 years ago by ★ 1.3k • written 8.1 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
8.3 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 8.4 years ago by ▴ 120 • written 8.4 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
8.4 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 8.4 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 8.4 years ago by ★ 1.3k • written 8.4 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 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
3
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8
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2.2k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
3
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3
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1.5k
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makeVRangesFromGRanges throws coercing "factor" to "NA" error
r packages somaticsignatures variantannotation
updated 8.5 years ago by 25k • written 8.5 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 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
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4
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2.1k
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Converting VCF to VRanges
somaticsignatures vranges
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
2
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8
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1.9k
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Regarding Somatic Mutation Signature
somaticsignatures
updated 8.6 years ago by ★ 1.3k • written 8.6 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
8.6 years ago user31888 ▴ 30
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8
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2.0k
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Regarding somatic signature package
somaticsignatures
updated 8.6 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 8.7 years ago by ★ 1.3k • written 8.7 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 8.7 years ago by ★ 1.3k • written 8.7 years ago by • 0
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1
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1.3k
views
Fitting somatic signatures to alexandrovs's
somaticsignatures somaticsignatures mutationcontext
updated 8.7 years ago by ★ 1.3k • written 8.7 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 8.7 years ago by ★ 11k • written 8.7 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
8.8 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 3 months ago by • 0 • written 8.8 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 8.8 years ago by ★ 1.3k • written 8.8 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
8.9 years ago • updated 8.8 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
8.9 years ago Jane Merlevede ▴ 90
0
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1
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1.3k
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SomaticSignatures: extract low level information
somaticsignatures somaticsignatures mutationcontext
updated 9.0 years ago by ★ 1.3k • written 9.0 years ago by • 0
0
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1
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1.8k
views
SomaticSignatures: negative entries after ComBat adjustment
sva somaticsignatures batch effect nmf
updated 9.1 years ago by ▴ 650 • written 9.1 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 • updated 9.3 years ago Asma rabe ▴ 290
3
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4
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1.7k
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Number of Signatures
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by ▴ 290
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4
replies
1.5k
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Assess number of Signatures in Somatic signatures
somaticsignatures
9.4 years ago Asma rabe ▴ 290
1
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3
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1.3k
views
nReplicates in Somatic Signatures
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 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
9.4 years ago Asma rabe ▴ 290
0
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1
reply
1.7k
views
.maf file in SomaticSignatures
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by • 0
2
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3
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1.8k
views
Determining number of signatures in SomaticSignatures
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by ▴ 30
4
votes
1
reply
1.4k
views
SomaticSignature - what samples contributed to each signature
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by ▴ 30
6
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12
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4.6k
views
SomaticSignatures: Compare my datas with validated mutational signatures
somaticsignatures mutational signature
updated 9.4 years ago by ▴ 30 • written 10.2 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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