Showing : RNAseq • reset
2
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2
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1.6k
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Failed assertion in subjunc aligner for large indels
rnaseq subjunc indel
updated 10.9 years ago by ★ 3.6k • written 10.9 years ago by ▴ 100
0
votes
3
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2.8k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 10.9 years ago by ★ 8.2k • written 10.9 years ago by ▴ 20
6
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2
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3.5k
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DESeq2: Excluding results of specific contrasts from another set of results
deseq2 rnaseq
11.0 years ago bmansfeld ▴ 10
2
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6
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7.4k
views
DESeq2: combine replicates following rlog transformation for visualization, clustering
deseq2 rnaseq
11.0 years ago snf ▴ 10
4
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5
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11k
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limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 10
2
votes
5
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4.3k
views
Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 11.0 years ago by ★ 3.4k • written 11.0 years ago by • 0
3
votes
2
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17k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 2.5 years ago by 53k • written 11.5 years ago by ★ 1.0k
2
votes
1
reply
1.9k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
21
votes
13
replies
17k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 50
3
votes
4
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3.3k
views
Probem in defining the design matrix for RNA-Seq analysis with edgeR
edger design and contrast matrix rnaseq
updated 11.0 years ago by ★ 29k • written 11.0 years ago by ▴ 20
0
votes
1
reply
4.1k
views
DESeq2 - factor base level changes the DE genes.
RNASeq Genetics DESeq2 RNASeq Genetics DESeq2
updated 11.0 years ago by 43k • written 11.3 years ago by ★ 13k
4
votes
3
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5.5k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
11.0 years ago gustavoborin01 • 0
3
votes
2
replies
3.1k
views
edgeR setting up glm/contrasts/ANOVA-like tests
edger rnaseq
updated 11.0 years ago by ★ 29k • written 11.0 years ago by ▴ 10
1
vote
3
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7.4k
views
Combat - error - system is computationally singular
combat software error rnaseq complex-design
updated 11.0 years ago by ★ 3.0k • written 11.0 years ago by ▴ 40
2
votes
3
replies
1.9k
views
edgeR error in dispCoxReid - no data rows with required number of counts
edger rnaseq error
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
0
votes
9
replies
3.2k
views
Multifactor analysis in EdgeR and DESeq2 - help setting up similar contrasts in the two packages
edger deseq2 rnaseq
11.0 years ago CT • 0
1
vote
1
reply
3.3k
views
How to use SamR
samr rnaseq CRAN
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 40
4
votes
7
replies
5.0k
views
Using DESeq2 with few biological replicates
deseq2 rnaseq
updated 11.0 years ago by ★ 3.8k • written 11.0 years ago by ▴ 100
1
vote
0
replies
890
views
GO analysis representation with RamiGO
go rnaseq
updated 11.0 years ago by 1.6k • written 11.0 years ago by ▴ 120
4
votes
2
replies
4.4k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 11.1 years ago by 1.6k • written 11.1 years ago by ▴ 270
12
votes
13
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9.2k
views
EdgeR Differential Expression analysis with NAs
EdgeR rnaseq NA
updated 11.1 years ago by ★ 29k • written 11.1 years ago by • 0
7
votes
1
reply
4.1k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 270
0
votes
8
replies
3.4k
views
Error in simpleLoess when running DEXSeq
DEX error simpleLoess RNAseq
updated 11.1 years ago by ★ 1.9k • written 11.1 years ago by ▴ 10
1
vote
3
replies
1.7k
views
Cell-type specific RNAseq analysis
rnaseq
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 120
0
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2
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1.5k
views
Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 11.1 years ago by 53k • written 11.1 years ago by ▴ 140
0
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1
reply
1.7k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
11.2 years ago Shi, Tao ▴ 720
1
vote
4
replies
2.6k
views
DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 11.2 years ago by ★ 1.9k • written 11.2 years ago by ▴ 650
0
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1
reply
4.9k
views
Steps of removing batch effects and hidden variables
RNASeq Normalization sva RNASeq Normalization sva
updated 11.2 years ago by ▴ 330 • written 11.2 years ago by ★ 1.0k
0
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1
reply
1.6k
views
DEXSeq continous variable in model
RNASeq GO DEXSeq DESeq2 RNASeq GO DEXSeq DESeq2
11.2 years ago Alex Gutteridge ▴ 650
0
votes
3
replies
1.6k
views
Goseq datasets
RNASeq GO goseq RNASeq GO goseq
11.2 years ago Eduardo Andres Leon ▴ 30
0
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0
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1.2k
views
compare RNASeq with Exon array data at the gene-level and exon-level
RNASeq Annotation RNASeq Annotation
11.2 years ago shirley zhang ★ 1.0k
0
votes
2
replies
2.3k
views
RNAseq expression threshold using DESeq2 normalised counts
RNASeq RNASeq
updated 11.2 years ago by 43k • written 11.2 years ago by ★ 13k
1
vote
3
replies
4.0k
views
[Help for DESeq]: Error in lfproc - newsplit: out of vertex space
RNASeq RNASeq
updated 11.2 years ago by ★ 13k • written 11.3 years ago by ▴ 20
1
vote
2
replies
2.8k
views
Interaction term logFC
RNASeq GO DESeq2 RNASeq GO DESeq2
updated 11.3 years ago by 68k • written 11.3 years ago by ★ 13k
2
votes
2
replies
2.2k
views
DESeq2: detect significantly increasing across an ordinal variable
RNASeq Cancer DESeq2 RNASeq Cancer DESeq2
updated 11.3 years ago by 43k • written 11.3 years ago by ▴ 100
0
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1
reply
1.8k
views
estimation of size factors in DESeq2 analysis
RNASeq DESeq DESeq2 RNASeq DESeq DESeq2
updated 11.3 years ago by 43k • written 11.3 years ago by ★ 1.5k
0
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6
replies
2.3k
views
SCAN.UPC for microarray and RNAseq data
RNASeq affy RNASeq affy
updated 11.3 years ago by ▴ 600 • written 11.3 years ago by ★ 1.0k
0
votes
3
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1.3k
views
DESeq analysis of resistance data
RNASeq Cancer DESeq2 RNASeq Cancer DESeq2
updated 11.3 years ago by 43k • written 11.3 years ago by ★ 13k
2
votes
2
replies
4.7k
views
readGappedAlignments not working in Rsamtools
RNASeq RNASeq
updated 11.3 years ago by ★ 6.8k • written 11.3 years ago by ★ 13k
0
votes
4
replies
1.9k
views
GenomicAlignments and QNAME collision
RNASeq Cancer convert Rsamtools GenomicAlignments RNASeq Cancer convert Rsamtools
updated 11.4 years ago by ▴ 90 • written 11.4 years ago by ★ 6.8k
0
votes
4
replies
1.9k
views
edgeR calcNormFactors for paired counts
RNASeq Normalization edgeR RNASeq Normalization edgeR
updated 11.4 years ago by ★ 7.9k • written 11.4 years ago by ▴ 210
0
votes
1
reply
1.4k
views
DEseq error
RNASeq DESeq RNASeq DESeq
updated 11.4 years ago by ★ 3.8k • written 11.4 years ago by ★ 13k
0
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0
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1.0k
views
[devteam-bioc] readGAlignmentPairs perfromace issue
RNASeq Cancer RNASeq Cancer
11.4 years ago Hervé Pagès 16k
0
votes
5
replies
2.9k
views
edgeR, logFC calculation in factor combination
RNASeq edgeR RNASeq edgeR
updated 11.4 years ago by 53k • written 11.4 years ago by ▴ 70
0
votes
1
reply
3.5k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
11.4 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
2
replies
1.5k
views
RNA-seq pathway analysis in Canis familiaris
RNASeq Genetics Annotation Canis familiaris gage RNASeq Genetics Annotation gage
updated 11.4 years ago by 68k • written 11.4 years ago by ▴ 140
0
votes
2
replies
1.1k
views
readGAlignmentPairs perfromace issue
RNASeq RNASeq
updated 11.4 years ago by ★ 6.8k • written 11.4 years ago by ★ 13k
0
votes
2
replies
2.7k
views
Best way of presenting "absolute" expression values (edgeR)
RNASeq edgeR RNASeq edgeR
updated 2.6 years ago by 53k • written 11.4 years ago by ▴ 110
0
votes
7
replies
1.6k
views
GenomicAlignments and QNAME collision
RNASeq GenomicAlignments RNASeq GenomicAlignments
updated 11.4 years ago by ★ 6.8k • written 11.4 years ago by ▴ 90
0
votes
0
replies
1.1k
views
RNA-Seq vs. Microarray
RNASeq Microarray Escherichia coli limma DESeq RNASeq Microarray Escherichia coli limma
11.5 years ago Willemijn van Mossevelde ▴ 10
1,409 results • Page 25 of 29
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Replies
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Votes
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
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