Showing : RNAseq • reset
5
votes
12
replies
2.8k
views
DESeq2 multi-factor comparison problem
deseq2 rnaseq
10.4 years ago Vivek.b ▴ 100
1
vote
9
replies
3.6k
views
RUV: removing unwanted variation in RNA-seq
RUV ruvseq rnaseq
10.4 years ago sergio.espeso-gil • 0
1
vote
4
replies
1.6k
views
Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 10.4 years ago by 43k • written 10.4 years ago by • 0
1
vote
0
replies
2.4k
views
Job: Postdoctoral Research Fellow in Bioinformatics - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
bioinformatician job rnaseq statistics systemsbiology Job
10.4 years ago Federico Marini ▴ 180
2
votes
2
replies
2.1k
views
Help with cummeRbund
cummeRbund Script analysis RNAseq cuffdiff
updated 10.4 years ago by ▴ 370 • written 10.4 years ago by • 0
0
votes
0
replies
1.4k
views
Biclustering approach to make transcription modules for rna seq data
rnaseq bicluster trancription modules eisa isa
10.4 years ago dhwani.dholakia • 0
2
votes
2
replies
1.2k
views
factorial linear modeling from DEseq2
deseq2 rnaseq differential gene expression
updated 10.5 years ago by ★ 13k • written 10.5 years ago by • 0
6
votes
3
replies
4.0k
views
Normalization of RNA-seq data, called remove unwanted variation (RUV), in DESeq2
normalization deseq2 rnaseq
10.5 years ago Silva • 0
0
votes
6
replies
3.4k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 10.5 years ago by ★ 1.6k • written 10.5 years ago by • 0
0
votes
2
replies
1.7k
views
EBSeq package gives NaN Values for EBMultiTest
differential expression ebseq rnaseq
10.5 years ago jbarker2 • 0
0
votes
1
reply
2.0k
views
RNASeq time-course analysis with maSigPro: T.fit error when assessing multiple groups
rnaseq masigpro timecourse
10.5 years ago Ryan Goosen • 0
0
votes
1
reply
957
views
MA plot error
rnaseq
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
7
votes
4
replies
7.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
10.5 years ago beiting ▴ 30
4
votes
8
replies
3.4k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 10
7
votes
4
replies
3.2k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 10
3
votes
7
replies
2.5k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 30
0
votes
1
reply
1.8k
views
Nested Comparison using DESeq2
deseq2 rnaseq
updated 10.5 years ago by ★ 7.9k • written 10.5 years ago by ▴ 60
0
votes
4
replies
17k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 10.5 years ago by 43k • written 10.5 years ago by ▴ 60
0
votes
3
replies
2.5k
views
How to analyze a known fusion gene expression in RNAseq
fusion genes rnaseq
10.5 years ago stephen66 ▴ 50
0
votes
2
replies
1.8k
views
Assessing RNA-Seq sample replicates
RNASeq
updated 10.5 years ago by ▴ 80 • written 12.6 years ago by ▴ 100
8
votes
4
replies
2.0k
views
Equivalence tests with edgeR
rnaseq edger equivalence
updated 10.5 years ago by ★ 29k • written 10.5 years ago by ▴ 20
2
votes
2
replies
3.9k
views
Down/Up-regulated genes asymmetry in edgeR differential expression analysis
edgeR rnaseq
10.5 years ago Pauly Lin ▴ 160
0
votes
1
reply
1.4k
views
edgeR MDS plot
RNASeq RNASeq
updated 10.6 years ago by 53k • written 13.6 years ago by ▴ 20
1
vote
5
replies
1.1k
views
matrix design and test advice
rnaseq
updated 10.6 years ago by ★ 29k • written 10.6 years ago by • 0
5
votes
7
replies
4.7k
views
How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
edger rnaseq glmlrt()
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
3
votes
5
replies
2.6k
views
PCA of voom weight values
limma voom rnaseq
updated 10.6 years ago by 53k • written 10.6 years ago by ▴ 140
18
votes
17
replies
5.5k
views
How to model a comparison between comparisons in edgeR?
edger rnaseq
updated 10.6 years ago by ★ 7.9k • written 10.6 years ago by ▴ 60
0
votes
0
replies
2.5k
views
Job: Abbvie -- Senior Manager/Associate Director, Exploratory Statistics
genomics genetics proteomics rnaseq microarray Job
10.6 years ago Feng Hong • 0
4
votes
4
replies
5.8k
views
Rsubread installation issues
rnaseq
10.6 years ago lshepard ▴ 40
0
votes
1
reply
2.0k
views
Job: Bioinformatics Post-Doc Positions
cancer BIOINFORMATICS genomics RNAseq miRseq Job
10.6 years ago aaron • 0
10
votes
10
replies
8.2k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 10.6 years ago by 53k • written 10.6 years ago by • 0
3
votes
4
replies
1.8k
views
DESeq2 detects DE when expression is 0 under both contrast levels
deseq2 rnaseq r
updated 10.6 years ago by 43k • written 10.6 years ago by • 0
3
votes
5
replies
6.0k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 10.7 years ago by ▴ 450 • written 10.7 years ago by ▴ 20
1
vote
1
reply
11k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 10.7 years ago by ★ 7.9k • written 10.7 years ago by ▴ 20
9
votes
8
replies
23k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 10.7 years ago by ▴ 610 • written 10.7 years ago by ▴ 20
4
votes
3
replies
1.3k
views
stacking (partially or completely overlapping) GRanges/IRanges
granges iranges rnaseq
updated 10.7 years ago by 25k • written 10.7 years ago by ★ 2.1k
5
votes
2
replies
7.8k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 10.7 years ago by ▴ 210 • written 10.7 years ago by ▴ 50
2
votes
2
replies
3.4k
views
DESeq2 design matrix for 6 groups
rnaseq deseq2 design and contrast matrix
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 20
2
votes
2
replies
6.3k
views
DESeq2 factor design vs pair-wise comparison
deseq2 rnaseq
10.7 years ago shin.jx • 0
5
votes
12
replies
8.6k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.7 years ago by 53k • written 11.5 years ago by ★ 1.0k
5
votes
6
replies
7.7k
views
proper transformation for differential expression in normalized log expression data
tcga rnaseq deseq2 vsn edger
updated 10.8 years ago by 53k • written 10.8 years ago by • 0
0
votes
0
replies
2.1k
views
News: RNAseq data analysis courses: Torino (Italy) : Beginner course March 17-19 2015 & Advance Course April 14-16 2015
rnaseq mirna onechannelgui chimera News
10.8 years ago raffaele calogero ▴ 500
6
votes
14
replies
7.1k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.8 years ago by 53k • written 10.8 years ago by • 0
1
vote
2
replies
1.9k
views
edgeR design matrix question
edgeR limma rnaseq design and contrast matrix
updated 10.8 years ago by 53k • written 10.8 years ago by • 0
0
votes
0
replies
1.6k
views
CummeRbund error problem
software error cummerbund rnaseq
10.8 years ago ytanaka • 0
1
vote
7
replies
5.0k
views
DESeq2 outlier detection not filtering
DESeq2 outlier RNASeq
updated 10.8 years ago by 43k • written 10.8 years ago by • 0
0
votes
2
replies
2.3k
views
quasR - how are exon identifiers for exon counts determined
rnaseq exon quasr
updated 10.9 years ago by ★ 13k • written 10.9 years ago by • 0
0
votes
0
replies
1.2k
views
makeTranscriptDbFromGFF errors when loading bacterial genes from gff
genomicfeatures rnaseq
10.9 years ago agd27 • 0
9
votes
9
replies
6.1k
views
Voom on TCGA data shifts count distributions towards negative values
voom TCGA RNAseq
10.9 years ago paola.ostano ▴ 10
2
votes
6
replies
11k
views
Estimation of dispersion in DeSeq and DeSeq2
deseq deseq2 rnaseq
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 10
1,409 results • Page 24 of 29
Recent ...
Replies
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Votes
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Awards • All
Popular Question to abaed • 0
Popular Question to ubjw24 • 0
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to shepherl 4.2k
Locations • All
The city by the bay, 3 minutes ago
United States, 10 minutes ago
Spain, 19 minutes ago
Estonia, 1 hour ago
USA, Los Angeles, USC, 1 hour ago
Traffic: 739 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