0
votes
1
reply
1.9k
views
HTA analysis at transcript level
pd.hta.2.0 transcript differential gene expression
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 40
0
votes
5
replies
4.0k
views
coefficients meaning in time course analysis with DESeq2
deseq2 timecourse time course design and contrast matrix coefficient of variation
updated 10.2 years ago by 43k • written 10.2 years ago by ★ 1.5k
0
votes
2
replies
1.8k
views
DE genes over time with DESeq2
deseq2 timecourse design and contrast matrix
updated 22 months ago by ▴ 10 • written 10.2 years ago by ★ 1.5k
0
votes
1
reply
1.4k
views
Modeling a combination of synchronized and unsynchronized time points?
design matrix spline ns limma
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ★ 7.9k
0
votes
5
replies
2.0k
views
Complete chromosome losses and polyploidies
cn.mops polyploidy
10.2 years ago mikko.arvas • 0
2
votes
5
replies
1.9k
views
proper way to subset columns of a DEXSeqDataset object
DEXSeq
10.2 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
2
votes
2
replies
1.1k
views
Deseq2 using principle components on raw or log normalized counts as covariates
deseq2 rnaseq normalization
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
4
votes
7
replies
2.5k
views
Performance of different flavors of limma and edgeR as the sample size goes up
limma edgeR
10.4 years ago • updated 10.2 years ago Nik Tuzov ▴ 90
1
vote
5
replies
4.3k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
10.2 years ago marcus.stoiber • 0
2
votes
6
replies
2.2k
views
edgeR_robust: where are moderately expressed genes?
edger rnaseq microrna
updated 10.2 years ago by ★ 29k • written 10.2 years ago by • 0
0
votes
2
replies
1.6k
views
R package for molecule interactions?
r package function interactions
10.2 years ago amyfm ▴ 10
1
vote
0
replies
1.2k
views
OntoCAT loading errors
ontocat ontologies uberon
10.2 years ago kamiljaron ▴ 10
1
vote
2
replies
1.7k
views
How do i perform chi square test in r?
microarray chisquare bioconductor bioinformatics
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 10
0
votes
3
replies
2.4k
views
Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Cancer convert minfi Cancer convert minfi
updated 10.2 years ago by • 0 • written 11.9 years ago by ★ 6.5k
0
votes
0
replies
1.6k
views
Different amount of overlapping Peaks in ChIPpeakAnno-Package
chippeakanno findoverlaps venn diagram
10.2 years ago N. F. • 0
3
votes
9
replies
5.6k
views
Can DESeq2 deal with zero-inflated data
deseq2
updated 10.2 years ago by ★ 3.8k • written 10.2 years ago by • 0
2
votes
6
replies
2.7k
views
Identifying TF binding sites (Motifdb + TxDb.Hsapiens.UCSC.hg19.knownGene)
motifdb JASPAR transcription factor binding site
10.2 years ago Lisa Hopcroft ▴ 40
2
votes
13
replies
15k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
10.2 years ago frostbite907 • 0
4
votes
1
reply
2.4k
views
Counting Raw Reads with DiffBind
diffbind
updated 10.2 years ago by ▴ 670 • written 10.2 years ago by • 0
4
votes
4
replies
2.5k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 460
0
votes
2
replies
1.5k
views
CoverageView error (bug?)
CoverageView
10.2 years ago termanini ▴ 10
0
votes
1
reply
856
views
xy2indices in Affy package : nr or nc parameter
xy2indices affy
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
2
votes
3
replies
1.7k
views
Building a reduced BSgenome.Gallus.UCSC.galGal 4 from Bioconductor
r build genome chicken-sheme
10.2 years ago pertille • 0
1
vote
1
reply
1.2k
views
inconsistent default of file suffix
variantannotation rsamtools
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ▴ 80
0
votes
0
replies
993
views
News: AnnotationHub downtime Wed 11/4
news News
10.2 years ago Dan Tenenbaum ★ 8.2k
18
votes
4
replies
39k
views
FDR and padj in deseq and edger
deseq2 edger
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 80
0
votes
2
replies
1.6k
views
motifbreakR VariantAnnotation namespace error on reading vcf file
motifbreakR variantannotation
updated 10.2 years ago by ▴ 50 • written 10.2 years ago by ▴ 20
1
vote
2
replies
1.6k
views
Create Db for exon starts/ends using rtracklayer
rtracklayer gtf
10.2 years ago Mehmet Ilyas Cosacak • 0
9
votes
3
replies
5.6k
views
how to extract Granges not overlapping with other ganges?
Granges findoverlaps
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 50
2
votes
1
reply
915
views
csaw not up to date
csaw
updated 10.2 years ago by ★ 29k • written 10.2 years ago by • 0
0
votes
0
replies
1.6k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
10.2 years ago kbastard • 0
0
votes
0
replies
2.4k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
10.2 years ago Jaritz,Markus ▴ 20
0
votes
4
replies
2.6k
views
Using cn.MOPs to estimate CNVs in tumors without reference normal
cn.mops cnvtools tcga cnv
updated 10.2 years ago by ▴ 540 • written 10.2 years ago by ▴ 20
2
votes
4
replies
1.8k
views
vcountPattern for Pattern Contained within or Containing Subject
biostrings countpattern
10.2 years ago Dario Strbenac ★ 1.6k
0
votes
5
replies
2.4k
views
matchPattern in BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg19
updated 10.2 years ago by 16k • written 10.2 years ago by ★ 4.3k
2
votes
5
replies
2.2k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb canis familiaris
updated 10.2 years ago by 16k • written 10.2 years ago by ★ 3.4k
3
votes
8
replies
2.5k
views
problem with @ranges@start in DNAStringSet
vcf testthat dnastringset
10.2 years ago TimothéeFlutre ▴ 80
1
vote
1
reply
1.1k
views
fold change in deseq
deseq2
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 80
0
votes
2
replies
1.9k
views
rhdf5 installation issue on Windows 64bit
rhdf5 windows
10.2 years ago cyang227 • 0
0
votes
1
reply
1.3k
views
RNAseq with two conditions - need help!
rnaseq deseq2 newbie
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
3
votes
2
replies
2.2k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 50
1
vote
1
reply
1.7k
views
DeSeq help with PCA
deseq2 PCA
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
3
votes
7
replies
5.3k
views
goseq code after DESeq2 -NO IDEA!
goseq DESEQ2 RSTUDIO CODE
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Error in extractROWS(x, eval(filter, x))
variantannotation filtervcf
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 80
0
votes
4
replies
3.8k
views
Impossible to use goseq package - problem with geneLenDataBase
goseq geneLenDataBase bioclite rstudio
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 10
0
votes
1
reply
2.4k
views
Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 10.2 years ago by ★ 8.2k • written 10.2 years ago by • 0
1
vote
2
replies
1.2k
views
The distribution function for zero-altered negative binomial density produces a probability greater 1
VGAM pzanegbin
updated 10.2 years ago by ★ 7.9k • written 10.2 years ago by ▴ 30
0
votes
1
reply
3.0k
views
Input file of NGS data for Pathview
rnaseq pathview data visualization
updated 10.2 years ago by ★ 1.6k • written 10.3 years ago by ▴ 10
0
votes
0
replies
1.6k
views
NOISeq error message while using ARSyNseq batch correction function
noiseq batch effect ARSyNseq
10.2 years ago lina.faller ▴ 10
0
votes
5
replies
2.6k
views
openCyto fails to load
opencyto bioclite
updated 10.2 years ago by • 0 • written 10.3 years ago by ▴ 20
46,730 results • Page 430 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: 697 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