0
votes
1
reply
1.5k
views
How to use GO.db select on *ANCESTOR *CHILDREN *PARENTS etc.
GO.db
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
0
replies
1.3k
views
WGCNA error during network construction
WGCNA Network R
4.3 years ago gitanjali • 0
0
votes
1
reply
1.7k
views
error in champ.norm
champ.norm ChAMP
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
1
vote
5
replies
3.2k
views
FELLA package - How to obtain the KEGG IDs that mapped to a pathway
fella
updated 4.2 years ago by ▴ 20 • written 6.9 years ago by • 0
0
votes
3
replies
4.6k
views
DESeq2 error in design~ code
DESeq2
4.3 years ago Abdou-samad • 0
0
votes
0
replies
1.2k
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
4.3 years ago alexandre.blais ▴ 50
0
votes
8
replies
2.3k
views
Three conditions and two time points
DifferentialExpression DESeq2 time
4.3 years ago • updated 4.2 years ago AZ ▴ 20
0
votes
0
replies
1.3k
views
DiffBind dba.counts memory issue
DiffBind
4.3 years ago rreese2 • 0
4
votes
2
replies
1.7k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
4.3 years ago Guillaume Devailly ▴ 60
0
votes
2
replies
2.3k
views
how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
updated 4.3 years ago by ★ 5.2k • written 4.4 years ago by • 0
1
vote
1
reply
1.6k
views
spearman correlation
correlation sperarman
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
0
votes
4
replies
5.0k
views
Question on the fold change estimate
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Senior/Principal Research Scientist in Computational Biology at Abbvie
Computational Bioinformatics
4.3 years ago Arch • 0
2
votes
4
replies
1.5k
views
Remove genes in a list from cts
DESeq2
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by ▴ 50
0
votes
0
replies
992
views
Fastest way to work with a large RangedSummarizedExperiment object
SummarizedExperiment summ
4.3 years ago alexgutteridge ▴ 50
2
votes
2
replies
1.8k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
4.3 years ago p.joshi ▴ 40
1
vote
5
replies
3.5k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
4.3 years ago Sonia • 0
0
votes
1
reply
5.0k
views
Error in curl; timeout when using biomaRt
biomaRt bioma
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by ▴ 10
0
votes
0
replies
957
views
Job: Flatiron Research Fellow, Structural and Molecular Biophysics
Research
4.3 years ago simonsF.careers • 0
0
votes
0
replies
1.3k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
4.3 years ago georgia.katsoula ▴ 40
0
votes
3
replies
1.6k
views
Details AnnotationTrack swap densityplot and connectors
Gviz
4.3 years ago Hartorthereal • 0
8
votes
9
replies
11k
views
Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
get_fun_from_pkg clusterProfiler rvcheck
updated 4.1 years ago by • 0 • written 4.3 years ago by • 0
1
vote
2
replies
1.9k
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
4.3 years ago Andrew Pattison • 0
1
vote
2
replies
1.4k
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
4.3 years ago • updated 4.0 years ago zeegzaag • 0
1
vote
4
replies
6.2k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.3 years ago Sandhiya • 0
4
votes
6
replies
2.7k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
4.3 years ago s-rhussien • 0
0
votes
0
replies
719
views
Formatting cellHTS2 experiment
cellHTS2
4.3 years ago yura.grabovska ▴ 30
3
votes
4
replies
1.7k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
4.3 years ago Rui ▴ 10
0
votes
1
reply
2.8k
views
Nested, multifactorial design formular for targeted contrast of a factor interaction
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
1
vote
3
replies
1.1k
views
[DESeq2] interaction term
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
1
vote
1
reply
1.2k
views
DESeq2 LRT test without a fixed base reference
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
920
views
DESeq2 (version 1.10 vs 1.30)
version1.30 version1.10 deseq2 DESeq2
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
0
votes
3
replies
3.9k
views
Installing SC3: gfortran error on Mac M1
SC3
4.3 years ago krp • 0
1
vote
1
reply
2.2k
views
Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 4.3 years ago by ★ 4.0k • written 6.5 years ago by ▴ 20
0
votes
2
replies
1.6k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
1
vote
3
replies
1.8k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Flatiron Research Fellow, Biophysical Modeling
Director
4.3 years ago simonsF.careers • 0
1
vote
3
replies
2.2k
views
Can VST be run without runing DESeq or estimateSizeFactors
DESeq2
4.3 years ago A ▴ 60
0
votes
2
replies
1.6k
views
How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
0
votes
1
reply
1.5k
views
slow lookup in SNPlocs.Hsapiens.dbSNP151.GRCh38 (or any SNPlocs package)
SNPlocs.Hsapiens.dbSNP151.GRCh38
updated 3.1 years ago by • 0 • written 4.3 years ago by ▴ 470
0
votes
6
replies
2.3k
views
GenomicScores package: availableGScores and getGScores functions not working
GenomicScores
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ▴ 20
0
votes
1
reply
2.5k
views
Unable to install Bioconductor packages
Bioconductor
updated 4.3 years ago by 4.3k • written 4.3 years ago by • 0
2
votes
1
reply
2.1k
views
Not able to Annotate CpG Island using methylKit
annotateWithGeneParts methylKit
4.3 years ago tanmayroy1979 ▴ 20
3
votes
5
replies
2.7k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
4
votes
8
replies
2.5k
views
deseq2 machine sizing best practices for very large data set
l DESeq2
updated 4.1 years ago by ▴ 20 • written 4.3 years ago by ▴ 20
1
vote
2
replies
1.8k
views
oligo package blas error
rma openblas blas oligo
4.3 years ago ch_el ▴ 10
0
votes
0
replies
1.3k
views
Job: Job: Moderna Statistical genomics co-op 2022, single-cell applications in immunology, masters or PhDs
co-op immunology single-cell omics
4.3 years ago joyce.hsiao1 • 0
1
vote
0
replies
802
views
Retrieve correlations to Module Eigengenes in CemiTool
CEMiTool
4.3 years ago Gilles ▴ 10
0
votes
1
reply
1.6k
views
branchpointer: trouble to read gtf
gtfToExons "Error:subscriptcontainsinvalidnames" gtf branchpointer
updated 4.3 years ago by • 0 • written 4.3 years ago by • 0
0
votes
0
replies
1.4k
views
News: BioC Asia Virtual Meeting, 1-4 November 2021
Workshop Asia BioCAsia Conference
4.3 years ago Peter Hickey ▴ 760
46,730 results • Page 112 of 935
Recent ...
Replies
Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
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
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
Germany, 12 minutes ago
United States, 1 hour ago
United States, 1 hour ago
The city by the bay, 2 hours ago
Barcelona, Spain, 4 hours ago
Traffic: 703 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6