2
votes
2
replies
561
views
simulateSV using Granges generates the error of "No regions on given chromosomes"
software error
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by ▴ 10
1
vote
1
reply
544
views
How to create a simple design matrix for limma
limma r
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
5
replies
5.3k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 840
0
votes
4
replies
2.8k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
5.8 years ago sibyl.bertrand • 0
0
votes
4
replies
1.8k
views
News: BridgeDb build fails due to website unavailability
bridgedbr News
6.1 years ago • updated 5.8 years ago egon.willighagen ▴ 10
3
votes
5
replies
15k
views
DESeq2 vs edgeR results analysis
deseq2 edgeR
updated 4.0 years ago by 53k • written 5.8 years ago by ▴ 40
1
vote
4
replies
2.4k
views
Data Structure for Read Count Analysis by DESeq2
deseq2 software error
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by ▴ 20
0
votes
8
replies
3.6k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
5.8 years ago felix.thaler • 0
0
votes
4
replies
1.7k
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
1
reply
723
views
DESeq2 error multifactiorial design
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
0
replies
1.4k
views
News: Import Deadlines for RELEASE 3.11
release devel deadline bioconductor News
5.8 years ago shepherl 4.3k
1
vote
2
replies
737
views
A gene is only expressed in one sample, and DESeq2 counts it as a DEG. Is this reasonable? How to deal with individual differences?
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
1.3k
views
Direct interactions in graphite ?
graphite interaction
updated 5.8 years ago by ▴ 100 • written 5.8 years ago by • 0
1
vote
2
replies
909
views
Data Structure for Read Count Analysis by DESeq2
deseq2 software error
updated 5.8 years ago by ▴ 10 • written 5.8 years ago by ▴ 20
0
votes
2
replies
1.2k
views
Qsea - plotCoverage
Qsea
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by ▴ 20
1
vote
11
replies
1.6k
views
Finding genes with loss of Heterozygosity
genomicrange
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by ▴ 20
0
votes
1
reply
930
views
ExpressionSet: any shortcut for number-of-samples and number-of-features?
expressionSet
5.8 years ago aush ▴ 40
0
votes
1
reply
842
views
deseq2 for enrichments between different subcellular fractions?
deseq2 galaxy
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
0
replies
2.1k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
2
votes
4
replies
7.5k
views
Error while installing hdf5 via BiocManager
software error
updated 5.8 years ago by ★ 6.6k • written 5.8 years ago by ▴ 20
1
vote
2
replies
723
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1
biomart
5.8 years ago xiaolei.zhou • 0
0
votes
4
replies
3.3k
views
Error in installing BiocManager
software error
5.8 years ago biok0423 ▴ 20
0
votes
1
reply
780
views
ATACseqQC and Rsamtools scanBam
software error
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
4
replies
2.2k
views
Error package or namespace load failed for DESeq2
deseq2
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
1
reply
812
views
Having issues generating manhattan plot in deseq2
deseq2 RNA-seq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
1
reply
1.4k
views
Biostrings matchPattern with lower case
biostrings
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Export Results from BatchQC Shiny App
BatchQC RNA-seq R Shiny batch-effect
5.8 years ago manninm • 0
0
votes
5
replies
3.5k
views
Using raw pvalue instead of adjusted pvalue in Deseq 2
DESeq2 RNA-seq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
3
replies
2.4k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
3
replies
739
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2 normalization
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
8
replies
2.2k
views
Weird MA-plot (DESeq2)
deseq2 RNAseq
5.8 years ago jgarces • 0
0
votes
11
replies
2.4k
views
DESeq2 contrast and complex comparisons
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 100
0
votes
34
replies
12k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 5.8 years ago by • 0 • written 6.3 years ago by • 0
0
votes
1
reply
1.4k
views
3x2 factorial design
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 30
0
votes
7
replies
1.1k
views
Highly differentially expressed genes having zero expression in one of the conditions lose significance if batch is added to the model in DESeq2
deseq2
5.8 years ago leonfodoulian • 0
0
votes
0
replies
885
views
Help about MSstats in skyline
Skyline.MS MSstats R
5.8 years ago pokhf123 • 0
0
votes
2
replies
2.4k
views
error in creating kallisto index
kallisto
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 20
1
vote
4
replies
3.7k
views
Issue with Biomart- cannot access ensembl
biomaRT
updated 16 months ago by • 0 • written 5.8 years ago by • 0
0
votes
2
replies
1.7k
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2 normalization
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
0
votes
1
reply
3.9k
views
DESeq2 with continuous variable
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
325
views
issue with resultsNames and contrast function
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
0
replies
856
views
Detect unique deletions in DNAMultipleAlignment
biostrings
5.8 years ago multipleseqs • 0
0
votes
4
replies
2.0k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon tximport tximportdata ensembl
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
1.2k
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 30
0
votes
0
replies
926
views
Bug(?) with GUID
flowAI software error
5.8 years ago christopher.hall • 0
0
votes
1
reply
1.3k
views
can download the r packages via crane
software error
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
1
vote
2
replies
2.0k
views
getBM biomart ensembl Error report
biomaRt ensembl
updated 5.8 years ago by ★ 6.6k • written 5.8 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
4
replies
3.1k
views
DESeq2 Error: package or namespace load failed for 'DESeq2'
RNA-Seq DESeq2
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by ▴ 10
0
votes
5
replies
4.9k
views
Error in (function (classes, fdef, mtable)
software error DECIPHER
updated 5.8 years ago by 4.3k • written 5.8 years ago by • 0
46,729 results • Page 170 of 935
Recent ...
Replies
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You may want to speak with a local statistician, because you don't just want to find the first full rank matrix and run with that if it doe…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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