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Showing :
somaticsignatures
•
reset
2
votes
7
replies
2.7k
views
SomaticSignatures, cannot reproduce use case
somaticsignatures
'IRanges
9.5 years ago
Anna N.
• 0
0
votes
6
replies
1.6k
views
SomaticSignatures: Interpretation of plotSamples graphs
somaticsignatures
8.2 years ago
Jane Merlevede
▴ 90
2
votes
6
replies
3.3k
views
Import of vcf with VariantAnnotation
variantannotation
somaticsignatures
9.5 years ago
Anna N.
• 0
0
votes
8
replies
2.3k
views
SomaticSignatures
Cancer
SomaticSignatures
Cancer
SomaticSignatures
updated 10.0 years ago by
Julian Gehring
★ 1.3k • written 10.1 years ago by
Dan Tenenbaum
★ 8.2k
2
votes
3
replies
1.3k
views
SomaticSignatures package : motifMatrix function trouble
somaticsignatures
6.8 years ago
guillaume.dachy
• 0
3
votes
4
replies
3.5k
views
Error while running SomaticSignatures
somaticsignatures
updated 7.7 years ago by
Andy Lynch
▴ 120 • written 7.7 years ago by
poojitha.ojamies
• 0
0
votes
6
replies
2.8k
views
Somaticsignature NMF problem
somaticsignatures
NMF
updated 6.5 years ago by
grimmmmer
• 0 • written 7.2 years ago by
ns
• 0
1
vote
7
replies
1.2k
views
Help creating VRange object
vcf
somaticSignatures
Vrange
updated 5.0 years ago by
Julian Gehring
★ 1.3k • written 5.0 years ago by
maisapinheiro12
• 0
6
votes
12
replies
4.1k
views
SomaticSignatures: Compare my datas with validated mutational signatures
somaticsignatures
mutational signature
updated 8.8 years ago by
chang02_23
▴ 30 • written 9.5 years ago by
muller.etienne
▴ 30
1
vote
10
replies
1.6k
views
SomaticSignatures nmfSignatures error
somaticsignatures
9.5 years ago
Francesc Castro
▴ 20
2
votes
6
replies
1.8k
views
SomaticSignatures low mutation rates
somaticsignatures
9.5 years ago
Francesc Castro
▴ 20
0
votes
8
replies
1.7k
views
Regarding somatic signature package
somaticsignatures
updated 8.0 years ago by
Julian Gehring
★ 1.3k • written 8.0 years ago by
sj1
▴ 10
2
votes
2
replies
1.0k
views
geom problem with SomaticSignatures plotRainfall
SomaticSignatures
updated 8.0 years ago by
Julian Gehring
★ 1.3k • written 8.0 years ago by
fourie.joubert
▴ 20
0
votes
2
replies
1.1k
views
SomaticSignatures: properties of the estimated signatures
somaticsignatures
8.2 years ago
Jane Merlevede
▴ 90
0
votes
2
replies
1.5k
views
Number of Signatures in SomaticSignatures package
SomaticSignatures
8.8 years ago
Asma rabe
▴ 290
2
votes
8
replies
1.6k
views
Regarding Somatic Mutation Signature
somaticsignatures
updated 8.0 years ago by
Julian Gehring
★ 1.3k • written 8.0 years ago by
sj1
▴ 10
1
vote
4
replies
1.8k
views
Converting VCF to VRanges
somaticsignatures
vranges
updated 7.8 years ago by
Julian Gehring
★ 1.3k • written 7.8 years ago by
arsala521
▴ 10
0
votes
3
replies
1.3k
views
Sequence Context of Somatic Variants
somaticsignatures
mutation context
updated 7.8 years ago by
Julian Gehring
★ 1.3k • written 7.8 years ago by
arsala521
▴ 10
3
votes
3
replies
1.3k
views
makeVRangesFromGRanges throws coercing "factor" to "NA" error
r packages
somaticsignatures
variantannotation
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
solo7773
▴ 10
3
votes
8
replies
1.9k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation
somaticsignatures
updated 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
maria.vila
• 0
1
vote
2
replies
1.1k
views
motifMatrix input object type, confused VRange and GRange
somaticsignatures
updated 7.8 years ago by
Julian Gehring
★ 1.3k • written 7.8 years ago by
solo7773
▴ 10
0
votes
2
replies
1.0k
views
Number of tumor samples and analysis by SomaticSignature Package
somaticsignatures
updated 7.8 years ago by
Julian Gehring
★ 1.3k • written 7.8 years ago by
arsala521
▴ 10
0
votes
1
reply
960
views
Input files for somaticSignature
somaticsignatures
updated 7.8 years ago by
Julian Gehring
★ 1.3k • written 7.8 years ago by
poojitha.ojamies
• 0
0
votes
1
reply
1.1k
views
Questions about SomaticSignatures packages
SomaticSignatures
updated 7.2 years ago by
Wolfgang Huber
★ 13k • written 7.2 years ago by
zzsu1999
• 0
0
votes
4
replies
3.5k
views
Installation of SomaticSignatures
SomaticSignatures
SomaticSignatures
updated 10.0 years ago by
Julian Gehring
★ 1.3k • written 10.0 years ago by
Guest User
★ 13k
2
votes
1
reply
955
views
SomaticSignatures objects in new version
somaticsignatures
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
Dave Wettmann
▴ 40
4
votes
1
reply
1.2k
views
SomaticSignature - what samples contributed to each signature
somaticsignatures
updated 8.8 years ago by
Julian Gehring
★ 1.3k • written 8.8 years ago by
chang02_23
▴ 30
2
votes
3
replies
1.6k
views
Determining number of signatures in SomaticSignatures
somaticsignatures
updated 8.8 years ago by
Julian Gehring
★ 1.3k • written 8.8 years ago by
chang02_23
▴ 30
0
votes
1
reply
1.5k
views
.maf file in SomaticSignatures
somaticsignatures
updated 8.8 years ago by
Julian Gehring
★ 1.3k • written 8.8 years ago by
Mega
• 0
1
vote
3
replies
1.1k
views
nReplicates in Somatic Signatures
somaticsignatures
updated 8.7 years ago by
Julian Gehring
★ 1.3k • written 8.7 years ago by
Asma rabe
▴ 290
3
votes
4
replies
1.5k
views
Number of Signatures
somaticsignatures
updated 8.7 years ago by
Julian Gehring
★ 1.3k • written 8.7 years ago by
Asma rabe
▴ 290
0
votes
1
reply
1.6k
views
SomaticSignatures: negative entries after ComBat adjustment
sva
somaticsignatures
batch effect
nmf
updated 8.4 years ago by
Jeff Leek
▴ 650 • written 8.4 years ago by
kw10
• 0
0
votes
1
reply
1.1k
views
SomaticSignatures: extract low level information
somaticsignatures
somaticsignatures mutationcontext
updated 8.4 years ago by
Julian Gehring
★ 1.3k • written 8.4 years ago by
mathieu.bourgey
• 0
0
votes
1
reply
1.1k
views
specify the color in plotMutationSpectrum() of SomaticSignatures library
SomaticSignatures
updated 8.1 years ago by
Julian Gehring
★ 1.3k • written 8.2 years ago by
sun
▴ 100
0
votes
1
reply
1.5k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.1 years ago by
Julian Gehring
★ 1.3k • written 8.1 years ago by
jolligoodfellow
• 0
1
vote
2
replies
1.5k
views
Combining GRange/VRange objects
granges
vranges
readvcfasvranges
somaticsignatures
updated 8.1 years ago by
Michael Lawrence
★ 11k • written 8.1 years ago by
jpluta26
• 0
0
votes
1
reply
1.1k
views
Fitting somatic signatures to alexandrovs's
somaticsignatures
somaticsignatures mutationcontext
updated 8.0 years ago by
Julian Gehring
★ 1.3k • written 8.0 years ago by
jolligoodfellow
• 0
1
vote
1
reply
1.1k
views
Contribution of Signature in each sample
mutational signature
somaticSignatures
updated 8.0 years ago by
Julian Gehring
★ 1.3k • written 8.0 years ago by
ksivapra
• 0
0
votes
1
reply
1.4k
views
How to compare SomaticSignatures package profiles with signatures listed by the Sanger Institute
somaticsignatures
updated 7.5 years ago by
Julian Gehring
★ 1.3k • written 7.5 years ago by
jonessara770
▴ 10
0
votes
1
reply
1.0k
views
plotMutationSpectrum Colour By Patient with Multiple Samples
plotMutationSpectrum
somaticsignatures
somaticsignatures package
updated 6.8 years ago by
Julian Gehring
★ 1.3k • written 6.8 years ago by
bruce.moran
▴ 30
1
vote
2
replies
1.6k
views
Trouble while concatenating VRanges object ()
somaticsignatures
somaticsignatures package
readvcfasvranges
vranges
6.7 years ago • updated 6.6 years ago
guillaume.dachy
• 0
0
votes
1
reply
1.0k
views
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 6.1 years ago by
shepherl
3.8k • written 6.1 years ago by
samuel.fux
• 0
0
votes
7
replies
3.0k
views
nmf function not working
somaticsignatures
NMF
updated 5.5 years ago by
Xin
• 0 • written 5.8 years ago by
aslam.mohammed398
• 0
0
votes
4
replies
1.5k
views
Error of read in large vcf file using readVcf
SomaticSignatures
VariantAnnotation
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
xiw588
• 0
0
votes
1
reply
1.5k
views
Questions about SomaticSignatures package
somaticsignatures
8.7 years ago
Asma rabe
▴ 290
0
votes
5
replies
1.6k
views
SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
somaticsignatures
somaticsignatures package
7.0 years ago
morovatunc
• 0
0
votes
4
replies
1.3k
views
Assess number of Signatures in Somatic signatures
somaticsignatures
8.7 years ago
Asma rabe
▴ 290
0
votes
5
replies
1.5k
views
Somatic Signature only SNV supported
somaticsignatures
5.5 years ago
TRASA
• 0
0
votes
0
replies
716
views
SomaticSignatures package: how can I get probability of certain mutation type within a signature?
somaticsignatures
5.4 years ago
spr
▴ 10
0
votes
4
replies
1.8k
views
SomaticSignatures: Compare my signatures with published COSMIC datasets
somaticsignatures
6.7 years ago
john.alexander
• 0
50 results • Page
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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