0
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2
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1.5k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
5.8 years ago • updated 5.2 years ago Nala • 0
1
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1
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1.8k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
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updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
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1
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2.3k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.2 years ago by ★ 5.2k
1
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4
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1.1k
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Using DESeq with 2 assays having 2 conditions
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5.2 years ago ludovic.malet • 0
1
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0
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905
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Error in peak calling with Combp
ENmix
5.2 years ago mwjnorris ▴ 10
0
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1
reply
2.3k
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How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
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4
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2.1k
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Raw reads count matrix from exceRpt pipeline are not integers which is needed for Deseq2
DESeq2 exceRpt exRNA
updated 5.2 years ago by ★ 1.1k • written 5.2 years ago by ▴ 10
3
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5
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4.0k
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csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 5.2 years ago by ▴ 10 • written 5.3 years ago by ▴ 50
1
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1
reply
1.4k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 5.2 years ago by 1.6k • written 5.2 years ago by ▴ 10
4
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0
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1.5k
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News: Bioconductor 3.12 is Released!
Software release Bioconductor Packages Release
5.2 years ago shepherl 4.3k
0
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3
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2.4k
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GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 5.2 years ago by ★ 3.4k • written 5.3 years ago by ▴ 70
4
votes
1
reply
2.0k
views
Changing Row Names of MultiAssayExperiment Assay
MultiAssayExperiment
updated 5.2 years ago by ▴ 100 • written 5.2 years ago by ★ 1.6k
3
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5
replies
3.5k
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Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 10
1
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1
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2.3k
views
DiffBind for ATAC-Seq count extraction
esATAC edgeR DiffBind
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by • 0
1
vote
10
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4.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.2 years ago by ★ 5.2k • written 5.3 years ago by ▴ 70
2
votes
2
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1.3k
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log transform or not the dependent variable/ covariates
limma edgeR
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 40
4
votes
10
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2.2k
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.2 years ago Hajar • 0
0
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1
reply
2.4k
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convert from profile to centroid.
MassSpectrometry xcms
updated 5.2 years ago by 1.6k • written 5.2 years ago by • 0
4
votes
8
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3.5k
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How DiffBind run PCA based on peak data?
DiffBind
updated 5.2 years ago by ★ 5.2k • written 8.4 years ago by ▴ 20
0
votes
0
replies
1.1k
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Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
5.2 years ago martinag.work • 0
0
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0
replies
1.0k
views
Weird behaviour with timescape package
timescape
5.2 years ago Graeme Thorn ▴ 10
1
vote
5
replies
2.1k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 5.2 years ago by • 0 • written 5.3 years ago by ▴ 10
0
votes
3
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1.7k
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Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 5.2 years ago by 43k • written 5.3 years ago by • 0
1
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1
reply
2.3k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 10
0
votes
0
replies
1.4k
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Job: Postdoctoral Data Scientist @ Oxford University, UK
Cancer CancerSubtypes postdoc
5.2 years ago Daniel Brewer ▴ 100
0
votes
3
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1.4k
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Bioconductor Git trouble to make push to KnowSeq Package at Release_3_11 branch
KnowSeq
5.3 years ago • updated 5.2 years ago daniel • 0
2
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2
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1.4k
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Paired analysis adjusted for RIN value
limma edgeR
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 40
0
votes
8
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2.8k
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flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow flowCore
updated 2.4 years ago by • 0 • written 5.3 years ago by ▴ 30
0
votes
0
replies
977
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Looking for a package to efficiently plot Hi-C contact maps
HiC hicrep HiCcompare
5.2 years ago changxu.fan ▴ 20
3
votes
3
replies
3.3k
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What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 60
4
votes
5
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3.1k
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emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 5.3 years ago by ★ 29k • written 6.4 years ago by ▴ 140
1
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3
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1.4k
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After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI Biobase
5.3 years ago Axel Klenk ★ 1.1k
4
votes
3
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2.5k
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catchSalmon for tx-level DE
catchSalmon edgeR
updated 2.2 years ago by 53k • written 5.3 years ago by ★ 5.0k
9
votes
10
replies
9.9k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.9 years ago by ▴ 20 • written 5.3 years ago by ▴ 10
10
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2
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1.4k
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News: SUPPORT SITE UPGRADE COMPLETE
SupportSite
updated 5.3 years ago by ★ 13k • written 5.3 years ago by 4.3k
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4
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3.1k
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Cannot properly finish biomaRt query
software error annotation biomart
updated 5.3 years ago by • 0 • written 5.6 years ago by ▴ 30
2
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1
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993
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The best pacakge to annotate a set of regions
annotate
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 20
1
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2
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diffbind error in sum(sapply(peaks, nrow)) : invalid 'type' (list) of argument
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.3 years ago by • 0
0
votes
11
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2.9k
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DESeq2 --- differences in log2FC between results from DESeq() command and nbinomLRT() command
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
0
replies
1.2k
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News: SUPPORT SITE UPGRADE TODAY -- PLEASE REFRAIN FROM POSTING
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5.3 years ago shepherl 4.3k
0
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1
reply
1.2k
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p-value/p-adj value as 0
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
4
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1.2k
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DESeq2 different datasets
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
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0
replies
691
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Differential gene expression associated with metabolite levels following diet
edger
5.3 years ago anna.cot.anna.cot ▴ 40
2
votes
3
replies
1.5k
views
DESeq2 multiple groups comparison issues, incorrect log2FC results in a small proportion of genes
deseq2
updated 5.2 years ago by 43k • written 5.3 years ago by • 0
1
vote
1
reply
1.3k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by • 0
0
votes
1
reply
919
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copynumber package issue
copynumber
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
1
vote
3
replies
2.8k
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copy number variation analysis (CNV)
copynumber plot visualization NGS gene
updated 5.1 years ago by ▴ 220 • written 5.3 years ago by • 0
0
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1
reply
1.1k
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 50
0
votes
1
reply
1.4k
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 5.3 years ago by ★ 1.1k • written 5.3 years ago by • 0
1
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2
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2.0k
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News: Final List of Deprecated Packages for Bioc3.12
annotation software experimentdata deprecated News
5.3 years ago shepherl 4.3k
46,730 results • Page 149 of 935
Recent ...
Replies
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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