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12
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2
answers
7.0k
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8 follow
2
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Differential expression analysis starting from TPM data
R tpm written 20 months ago by cahidora • 20 • updated 20 months ago by Gordon Smyth ♦ 37k
5
votes
1
answer
963
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6 follow
1
answer
WGCNA - looking for over-representation of DEGs within gene networks
wgcna R bioconductor differential gene expression written 3.3 years ago by sm15766 • 30 • updated 3.3 years ago by Peter Langfelder • 1.8k
8
votes
2
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830
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6 follow
2
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Any method can coerce "list" object to GRanges [reproducible example is included]?
granges R error handling written 3.1 years ago by Jurat Shahidin • 60 • updated 3.1 years ago by Michael Lawrence ♦ 10k
8
votes
1
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5.9k
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6 follow
1
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DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 R written 2.3 years ago by tombernardryan • 30 • updated 2.3 years ago by Michael Love ♦ 22k
3
votes
2
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8.8k
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5 follow
2
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Integrating DESeq2 and TopGO for Enrichment
rnaseq go deseq2 R written 4.2 years ago by nw328 • 10 • updated 4.2 years ago by Bernd Klaus • 540
5
votes
3
answers
3.4k
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5 follow
3
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sqliteSendQuery error in AnnotationForge bioconductor package
annotation annotationdbi annotationforge R bioconductor written 4.2 years ago by Stephen H • 0 • updated 2.8 years ago by Axel Klenk • 920
8
votes
3
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4.3k
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5 follow
3
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could not find symbol "keepNA" in environment of the generic function
genomicranges genomicalignments R summarizeoverlaps function written 3.8 years ago by Assa Yeroslaviz • 1.4k • updated 3.8 years ago by Mathilde • 0
0
votes
1
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917
views
5 follow
1
answer
Normalisation of RNA seq data
rnaseq normalization R bioconductor written 3.2 years ago by Fiona • 70 • updated 3.1 years ago by chris86 • 380
1
vote
5
answers
1.2k
views
5 follow
5
answers
problem with makeOrgPackageFromNCBI when making an annotation package
annotationforge R bioconductor written 2.7 years ago by wssdandan2009 • 0 • updated 2.3 years ago by theobroma22 • 10
2
votes
0
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604
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5 follow
0
answers
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
pathways job R bioinformatician job phd written 2.6 years ago by Frank Kramer • 60
5
votes
0
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621
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5 follow
0
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Job: Summer Studentships in Data Science (Computational Cancer Biology) at the University of Cambridge
job R python machine learning cancer genomics deep learning written 2.0 years ago by Shamith.Samarajiwa • 150
6
votes
2
answers
765
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2
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permutation test against intervals
R pkg written 4.1 years ago by csc.csclogin.login40 • 20 • updated 3.9 years ago by bgel • 30
10
votes
2
answers
2.5k
views
2
answers
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
limma oligo R differential gene expression affymetrix microarrays written 3.8 years ago by dennis.oezcelik • 10 • updated 3.8 years ago by tree-ski • 0
6
votes
2
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5.4k
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2
answers
Heatmap Plotting in R
R bioconductor heatmap written 3.7 years ago by Deepak Tanwar • 10
0
votes
1
answer
953
views
1
answer
Plotting gene region using Sushi
R sushi written 3.2 years ago by javier.mendoza • 0 • updated 3.2 years ago by dphansti • 10
5
votes
2
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2.8k
views
2
answers
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges R split written 3.2 years ago by Jurat Shahidin • 60
6
votes
1
answer
1.4k
views
1
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deseq2 estimating size factors
deseq2 R written 3.0 years ago by gv • 40 • updated 3.0 years ago by Michael Love ♦ 22k
5
votes
1
answer
589
views
1
answer
seeking idea for proper output representation for multiple GRanges overlapping
biocparallel grangeslist R findoverlaps written 2.8 years ago by Jurat Shahidin • 60
7
votes
4
answers
686
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4
answers
Test whether expression levels of two gene sets are significantly different
deseq2 R gene set testing gene expression written 2.4 years ago by Jon Bråte • 150
4
votes
2
answers
722
views
2
answers
xcms and xcmsSet no longer works on my Mac
R bioconductor written 2.4 years ago by nickpardikes • 0 • updated 2.4 years ago by Johannes Rainer • 1.4k
2
votes
1
answer
678
views
1
answer
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva R removebatcheffect written 23 months ago by aina.jene • 10 • updated 23 months ago by sina.nassiri • 70
7
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2
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2.0k
views
2
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R: error while reading .h5 files from R using rdhf5 package
rhdf5 R hdf5 written 22 months ago by him4u324 • 0 • updated 22 months ago by Wolfgang Huber ♦ 13k
5
votes
1
answer
762
views
1
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Please use the function 'listAttributes' to get valid attribute names
biomart R written 21 months ago by al14 • 0
8
votes
1
answer
6.3k
views
1
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LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq limma R logfc differential gene expression written 21 months ago by cms72 • 0 • updated 21 months ago by Aaron Lun • 23k
3
votes
0
answers
739
views
0
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Using sluth with Salmon data, error while sleuth_prep
R salmon sleuth salmon rna seq written 17 months ago by Walter F. Baumann • 10
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