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3
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limma voom accessing normalised counts tables
geneexpression rnaseq limma voom counts written 5.0 years ago by Peter Crisp • 10 • updated 5.0 years ago by Steve Lianoglou ♦ 12k
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Problem making DESeq dataset; Error all variables in design formula must be columns in colData
rnaseq deseq deseq2 counts differential gene expression written 3.5 years ago by wannes.nauwynck • 0 • updated 3.5 years ago by Michael Love ♦ 25k
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How do I extract read counts from DESeq2
deseq2 counts covariates written 3.6 years ago by hechtp • 0 • updated 3.6 years ago by Michael Love ♦ 25k
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Not full rank design using Deseq2
deseq2 counts design written 4.7 years ago by Rainy Gorilla • 20 • updated 4.7 years ago by Michael Love ♦ 25k
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Limma/DESeq2: Statistic and readcount of biological replicates
normalization limma deseq2 counts written 3.8 years ago by Radek • 60 • updated 3.8 years ago by Aaron Lun • 25k
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Can edgeR TMM normalization be used for other count data?
normalization edger counts tmm written 2.5 years ago by jol.espinoz • 20 • updated 2.5 years ago by James W. MacDonald ♦ 51k
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HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff written 3.7 years ago by Jon Bråte • 160
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chromosome name in summarizeOverlaps for RNASeq data
rnaseq annotation counts summarizeoverlaps written 3.8 years ago by bioprog • 0
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DESeq2 Input format
deseq2 counts written 3.1 years ago by uzer • 0 • updated 3.1 years ago by Michael Love ♦ 25k
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unable to find an inherited method for function counts for signature DESeqTransform
deseq2 counts variance deseqtransform deviation written 2.0 years ago by Casper Peters • 0 • updated 2.0 years ago by Michael Love ♦ 25k
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1
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deseq2 normalized data
regression deseq2 counts written 4.1 years ago by akp • 0 • updated 4.1 years ago by Michael Love ♦ 25k
4
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2
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898
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Help: extract counts from RNA-seq .bam/.bai files
edger counts written 2.4 years ago by mat149 • 40 • updated 2.4 years ago by Aaron Lun • 25k
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2
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Conversion from counts to FPKM
normalization deseq2 counts fpkm fpkm() written 10 months ago by chiara.facciotto • 0 • updated 7 months ago by Ahmed Alhendi • 0
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DEXSeq error: Count files do not correspond to the flattened annotation file
dexseq gff counts written 4.9 years ago by Assa Yeroslaviz • 1.4k
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733
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IRanges object from count matrix
rnaseq iranges genomicranges featurecounts counts written 2.7 years ago by Assa Yeroslaviz • 1.4k • updated 2.7 years ago by Hervé Pagès ♦♦ 14k
2
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708
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converting extremely sparse count dataframe to continuous distributions for study in WGCNA
voom counts limma voom written 3.2 years ago by chrisclarkson100 • 30 • updated 3.2 years ago by Gordon Smyth ♦ 39k
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688
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Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
chipseq deseq2 error counts log2fc written 3.4 years ago by robin.uchiyama • 0 • updated 3.4 years ago by Michael Love ♦ 25k
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DESeq2: Do basemean values take into account interaction effects?
deseq2 counts normalized counts written 3.2 years ago by snamjoshi87 • 30 • updated 3.2 years ago by Steve Lianoglou ♦ 12k
2
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Deseq2: padj value changes with varying alpha
rnaseq deseq2 counts written 24 months ago by yoursbassanio • 0 • updated 24 months ago by Michael Love ♦ 25k
3
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1
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543
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1
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window counts in csaw
counts csaw written 3.4 years ago by nobishvarghese • 0 • updated 3.4 years ago by Aaron Lun • 25k
1
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1
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519
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comparing transcripts expression between conditions
counts transcripts salmon significance written 3.3 years ago by Assa Yeroslaviz • 1.4k
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2
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497
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small RNAs quantification
smallrna counts written 3.1 years ago by ribioinfo • 90
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476
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DESeq2 ComputeSumFactors extract normalized counts
normalization deseq2 counts written 2.1 years ago by herrmannmaria94 • 0 • updated 2.1 years ago by Michael Love ♦ 25k
2
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1
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424
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1
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Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
chipseq diffbind counts bedtools peaks written 18 months ago by Ni-Ar • 0 • updated 17 months ago by Rory Stark • 2.9k
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400
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Handling pseudogenes in RNA-seq
counts star rna-seq pseudogenes written 16 months ago by supremerulersuraj • 0 • updated 16 months ago by Levi Waldron ♦ 950
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