3
votes
18
replies
3.8k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
18 months ago • updated 9 months ago shepherl 4.1k
0
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11
replies
1.7k
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
10 months ago • updated 12 weeks ago shepherl 4.1k
7
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28
replies
7.1k
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 months ago by 52k • written 9.9 years ago by ★ 7.9k
0
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12
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7.2k
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ChAMP input: Beta Matrix?
champ dmr analysis
updated 6 months ago by • 0 • written 8.9 years ago by • 0
16
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12
replies
7.9k
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Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 4 months ago by • 0 • written 8.8 years ago by ▴ 60
2
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6
replies
3.0k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 10 months ago by • 0 • written 7.0 years ago by ▴ 10
4
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5
replies
11k
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[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 5 months ago by • 0 • written 7.3 years ago by ▴ 60
14
votes
22
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31k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 10 months ago by 43k • written 8.6 years ago by ▴ 30
0
votes
7
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960
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DESeq2 filtering vs edgeR filtering
DESeq2
10 months ago • updated 9 months ago fr8712ca-s • 0
0
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9
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1.8k
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athPkgBuilder data source :missing probesets
Annotation Annotation
written 18.4 years ago by ▴ 870
0
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6
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3.5k
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limma, analysis on subset of data gives completely different results
limma limma
updated 9 months ago by 52k • written 10.5 years ago by ▴ 40
4
votes
16
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8.2k
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Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 9 months ago by • 0 • written 9.7 years ago by ▴ 160
3
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3
replies
3.7k
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maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 10 months ago by ▴ 200 • written 7.3 years ago by ▴ 100
0
votes
11
replies
4.6k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 11 months ago by ▴ 200 • written 7.8 years ago by ★ 2.0k
0
votes
6
replies
1.5k
views
LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
affy affy
updated 10 months ago by 52k • written 19.7 years ago by ★ 1.1k
2
votes
8
replies
949
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 9 months ago by 52k • written 9 months ago by • 0
6
votes
15
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1.5k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
5
replies
857
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 months ago by 52k • written 4 months ago by • 0
0
votes
11
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2.5k
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globaltest question
Pathways probe affy Pathways probe affy
written 18.4 years ago by ▴ 30
2
votes
3
replies
1.3k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 12 months ago by • 0 • written 3.5 years ago by ▴ 470
3
votes
12
replies
3.9k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 5 months ago by ▴ 200 • written 13 months ago by ▴ 10
0
votes
3
replies
1.3k
views
Limma - using both array and spot weights in lmFit
Genetics Genetics
written 17.7 years ago by ▴ 170
10
votes
11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 80
0
votes
44
replies
4.3k
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 8 months ago by 43k • written 23 months ago by • 0
1
vote
8
replies
1.2k
views
DEseq2 time-series design
deseq2
updated 3 months ago by ▴ 10 • written 5.8 years ago by • 0
4
votes
7
replies
1.3k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 5 months ago by ▴ 10 • written 6 months ago by ▴ 70
0
votes
4
replies
7.3k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 17 days ago by • 0 • written 2.4 years ago by • 0
9
votes
14
replies
7.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 6 months ago by 4.1k • written 3.0 years ago by ▴ 40
1
vote
3
replies
3.6k
views
WGNCA kME vs. kIM
WGCNA
updated 7 months ago by • 0 • written 9.3 years ago by ▴ 30
7
votes
6
replies
1.2k
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 8 months ago by • 0
1
vote
16
replies
4.5k
views
error in ChAMP loading file
ChAMP
updated 10 months ago by • 0 • written 2.2 years ago by • 0
10
votes
41
replies
7.5k
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Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 7 months ago by • 0 • written 6.1 years ago by ★ 4.1k
0
votes
5
replies
1.2k
views
Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 6 months ago by 4.1k • written 6 months ago by • 0
3
votes
11
replies
802
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
votes
5
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1.6k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
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updated 4 months ago by • 0 • written 4.3 years ago by ▴ 10
17
votes
9
replies
7.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 3 months ago by 67k • written 8.6 years ago by ▴ 10
0
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3
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2.4k
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maSigPro genes from clusters
masigpro clustering
updated 8 months ago by • 0 • written 8.6 years ago by • 0
8
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6
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921
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DGE analysis with LIMMA
limma
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
6
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1.5k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
2
votes
2
replies
5.1k
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Unable to install the package "tissuesGeneExpression"
bioconductor
updated 6 months ago by • 0 • written 7.5 years ago by ▴ 10
2
votes
2
replies
629
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Handling biological replicates in DESeq2
DESeq2
updated 8 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
0
votes
4
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 12 months ago by • 0
6
votes
6
replies
2.3k
views
limma plotMDS - logFC inverted?
limma MultidimensionalScaling
updated 4 months ago by 67k • written 2.1 years ago by • 0
1
vote
6
replies
997
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 9 weeks ago by 43k • written 9 weeks ago by ▴ 10
0
votes
6
replies
754
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 130
15
votes
17
replies
2.3k
views
Why p value inconsistent when using different number of pathway score?
limma
8 months ago Chris ▴ 20
5
votes
4
replies
516
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
0
votes
5
replies
10k
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tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 10 months ago by • 0 • written 8.3 years ago by • 0
3
votes
3
replies
13k
views
How to find rsID with biomaRt in R
biomaRt
updated 11 months ago by 67k • written 3.9 years ago by ▴ 10
5
votes
9
replies
2.0k
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Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 6 months ago by • 0
1,461 results • Page 1 of 30
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
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Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
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Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
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