0
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3
replies
933
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File type for DEseq using ATACseq data
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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2
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4.0k
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Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
2
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6
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2.8k
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RNA-Seq normalization for co-expression analysis
edger WGCNA limma
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 50
0
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2
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1.9k
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DESeq2 error on analyzing microbiome data
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6.6 years ago zhigang.li • 0
4
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5
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3.6k
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GDCprepare - error
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6.6 years ago vm ▴ 30
2
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3
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1.7k
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VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.6 years ago by ★ 11k • written 6.6 years ago by • 0
0
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3
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1.8k
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Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
0
votes
1
reply
482
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Retrieving Normalized Groups from Results()
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
1
reply
608
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Should I subsample an over-clustered sample for DESeq2?
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
6
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6
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1.6k
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EdgeR - Model matrix for complex model similar to user guide 3.5 example - but more complex
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updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
2
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2
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5.1k
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ClusterProfiler GSEA with geneList
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updated 6.6 years ago by ▴ 80 • written 6.6 years ago by • 0
0
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1
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1.4k
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CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf snv gatk customprodb inputvcf
6.6 years ago Elena.M • 0
3
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6
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2.5k
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Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 30
2
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2
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2.7k
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Finding genes in a gene set detected by ROAST (or FRY) in limma
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updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 20
5
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18
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2.9k
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Difference of difference, paired design
edger deseq2 limma
updated 6.6 years ago by ★ 1.4k • written 6.6 years ago by • 0
0
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2
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1.1k
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Master of Science
CNTools
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
2
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2
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2.1k
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TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 10
2
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1
reply
1.3k
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> DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
DiffBind R R Studio
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
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1
reply
1.3k
views
Using GoSemSim with other Ontologies
GOSemSim
updated 6.6 years ago by ▴ 760 • written 6.6 years ago by • 0
0
votes
0
replies
879
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sequence positions change in seqPattern plots with few matching sites
seqPattern
6.6 years ago danlu • 0
0
votes
1
reply
1.0k
views
find genes near a microRNA binding site
R microRNA genes binding Site
6.6 years ago pengu447 • 0
0
votes
0
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1.3k
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
6.6 years ago jmaanaki • 0
1
vote
2
replies
921
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Error in biomaRt query - "biomaRt expected a character string of length 1.
biomart R
updated 6.6 years ago by ▴ 10 • written 6.6 years ago by • 0
1
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0
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1.3k
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News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
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6.6 years ago Johannes Rainer ★ 2.1k
0
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2
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711
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Creating the correct design
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
5
replies
3.1k
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Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
2
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1
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921
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Using altHypothesis with shrunken LFC values in DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
5
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2.7k
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Paired samples in cell lines using DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
votes
3
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1.5k
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Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
2
replies
1.6k
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problem about using cn.mops
cn.mops
updated 4.7 years ago by • 0 • written 6.6 years ago by • 0
0
votes
4
replies
1.1k
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exomeCopy compileCopyCountSegments error
exomeCopy
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
27
votes
17
replies
10k
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DESeq2 1.20.0 lfcshrink function
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updated 4.7 years ago by 43k • written 7.6 years ago by ▴ 50
0
votes
3
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1.4k
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Replacement error in PermTest
regioneR
6.6 years ago AlejandroMA • 0
0
votes
6
replies
2.5k
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deseq2 pre filter rna seq
deseq2 rnaseq
updated 2.3 years ago by 43k • written 6.6 years ago by • 0
1
vote
9
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3.5k
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Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
1
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5
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929
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SummarizedExperiments error for reading the data
software error
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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0
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1.4k
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Including sva results in SeqGSEA with data with batch effect
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6.6 years ago kentfung ▴ 20
0
votes
2
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1.5k
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R: rma() function error
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updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
vote
3
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how to run old scripts using corresponding biomaRt versions from archives
biomaRt Bioconductor
updated 6.6 years ago by ★ 6.6k • written 6.6 years ago by ▴ 10
0
votes
1
reply
1.4k
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Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt
r
updated 6.6 years ago by ▴ 150 • written 6.6 years ago by • 0
0
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1
reply
2.8k
views
R: oligo packages install error
oligo packages error
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
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1
reply
3.1k
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Differential Methylation Analysis using ChAMP
ChAMP
updated 4 months ago by 43k • written 6.6 years ago by • 0
0
votes
1
reply
1.4k
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Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
6.6 years ago Boran Gao • 0
0
votes
1
reply
523
views
tximport in DESeq2 problem
tximport
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
4
replies
1.6k
views
Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma deseq2 edgeR
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 50
7
votes
44
replies
8.5k
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OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 6.6 years ago by 4.3k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.6k
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Model matrix for longitudinal pairwise rna-seq data: linear regression or linear mixed model?
limma model matrix linear regression
6.6 years ago agm • 0
0
votes
0
replies
1.1k
views
adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
votes
2
replies
4.5k
views
Anbiguous instruction on how to set the blind value in DESeq2's vst function
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
3
replies
1.8k
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 20
46,742 results • Page 205 of 935
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Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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