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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913
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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 6.1 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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890
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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
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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
7.4 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
7.4 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
7.5 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
8.2 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 8.2 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
8.3 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 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
0
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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 8.5 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
views
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
views
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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2.0k
views
Regarding Somatic Mutation Signature
somaticsignatures
updated 8.6 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 8.7 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
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
views
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
8.8 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
0
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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
views
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
reply
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
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Questions about SomaticSignatures package
somaticsignatures
9.4 years ago Asma rabe ▴ 290
3
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4
replies
1.7k
views
Number of Signatures
somaticsignatures
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by ▴ 290
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4
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1.5k
views
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
0
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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 9.5 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
replies
4.6k
views
SomaticSignatures: Compare my datas with validated mutational signatures
somaticsignatures mutational signature
updated 9.5 years ago by ▴ 30 • written 10.2 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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