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16
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2
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10k
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10 follow
2
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Differential expression analysis starting from TPM data
R tpm written 2.2 years ago by cahidora • 40 • updated 2.2 years ago by Gordon Smyth ♦ 39k
5
votes
1
answer
1.1k
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6 follow
1
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WGCNA - looking for over-representation of DEGs within gene networks
wgcna R bioconductor differential gene expression written 3.8 years ago by sm15766 • 30 • updated 3.8 years ago by Peter Langfelder • 2.2k
8
votes
2
answers
1.0k
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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 3.6 years ago by Jurat Shahidin • 70 • updated 3.6 years ago by Michael Lawrence ♦ 11k
8
votes
1
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8.3k
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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 2.8 years ago by tombernardryan • 30 • updated 2.8 years ago by Michael Love ♦ 25k
3
votes
2
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10k
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5 follow
2
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Integrating DESeq2 and TopGO for Enrichment
rnaseq go deseq2 R written 4.7 years ago by nw328 • 10 • updated 4.7 years ago by Bernd Klaus • 560
5
votes
3
answers
3.5k
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3
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sqliteSendQuery error in AnnotationForge bioconductor package
annotation annotationdbi annotationforge R bioconductor written 4.7 years ago by Stephen H • 0 • updated 3.3 years ago by Axel Klenk • 940
8
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3
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4.5k
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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 4.3 years ago by Assa Yeroslaviz • 1.4k • updated 4.3 years ago by Mathilde • 0
0
votes
1
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1.0k
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1
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Normalisation of RNA seq data
rnaseq normalization R bioconductor written 3.7 years ago by Fiona • 70 • updated 3.7 years ago by chris86 • 380
1
vote
5
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1.3k
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5 follow
5
answers
problem with makeOrgPackageFromNCBI when making an annotation package
annotationforge R bioconductor written 3.2 years ago by wssdandan2009 • 0 • updated 2.8 years ago by theobroma22 • 10
2
votes
0
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679
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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 3.1 years ago by Frank Kramer • 60
5
votes
0
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696
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5 follow
0
answers
Job: Summer Studentships in Data Science (Computational Cancer Biology) at the University of Cambridge
job R python machine learning cancer genomics deep learning written 2.5 years ago by Shamith.Samarajiwa • 180
8
votes
1
answer
8.9k
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5 follow
1
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LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq limma R logfc differential gene expression written 2.3 years ago by cms72 • 0 • updated 2.2 years ago by Aaron Lun • 25k
6
votes
2
answers
882
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2
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permutation test against intervals
R pkg written 4.6 years ago by csc.csclogin.login40 • 20 • updated 4.4 years ago by bgel • 30
10
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2
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2.6k
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2
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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 4.3 years ago by dennis.oezcelik • 10 • updated 4.3 years ago by tree-ski • 0
6
votes
2
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5.6k
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2
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Heatmap Plotting in R
R bioconductor heatmap written 4.2 years ago by Deepak Tanwar • 10
0
votes
1
answer
1.1k
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1
answer
Plotting gene region using Sushi
R sushi written 3.7 years ago by javier.mendoza • 0 • updated 3.7 years ago by dphansti • 10
5
votes
2
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3.2k
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2
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How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges R split written 3.7 years ago by Jurat Shahidin • 70
6
votes
1
answer
1.6k
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1
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deseq2 estimating size factors
deseq2 R written 3.5 years ago by gv • 40 • updated 3.5 years ago by Michael Love ♦ 25k
5
votes
1
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664
views
1
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seeking idea for proper output representation for multiple GRanges overlapping
biocparallel grangeslist R findoverlaps written 3.3 years ago by Jurat Shahidin • 70
7
votes
4
answers
795
views
4
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Test whether expression levels of two gene sets are significantly different
deseq2 R gene set testing gene expression written 2.9 years ago by Jon Bråte • 160
4
votes
2
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798
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2
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xcms and xcmsSet no longer works on my Mac
R bioconductor written 2.9 years ago by nickpardikes • 0 • updated 2.9 years ago by Johannes Rainer • 1.5k
2
votes
1
answer
799
views
1
answer
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva R removebatcheffect written 2.5 years ago by aina.jene • 10 • updated 2.4 years ago by sina.nassiri • 70
7
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2.8k
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2
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R: error while reading .h5 files from R using rdhf5 package
rhdf5 R hdf5 written 2.3 years ago by him4u324 • 0 • updated 2.3 years ago by Wolfgang Huber ♦ 13k
5
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1
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1.1k
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1
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Please use the function 'listAttributes' to get valid attribute names
biomart R written 2.3 years ago by al14 • 0
3
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0
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894
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0
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Using sluth with Salmon data, error while sleuth_prep
R salmon sleuth salmon rna seq written 23 months ago by Walter F. Baumann • 10
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