Showing : RNA-seq • reset
5
votes
2
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25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
vote
6
replies
931
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 4 weeks ago by 43k • written 4 weeks ago by ▴ 10
0
votes
2
replies
287
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
9 weeks ago paul.meraner • 0
0
votes
0
replies
197
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
11 weeks ago Fernanda • 0
1
vote
3
replies
566
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 months ago by 67k • written 6 months ago by ▴ 50
2
votes
4
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670
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
2
replies
628
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
7 months ago Dylan.Sheerin • 0
2
votes
5
replies
980
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 months ago by ★ 4.6k • written 7 months ago by • 0
3
votes
3
replies
908
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
1.1k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 12 months ago by ★ 4.6k • written 6.7 years ago by • 0
0
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2
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530
views
WGCNA less samples
RNA-Seq WGCNA Worms
12 months ago davca • 0
0
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4
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1.1k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
14 months ago ar14g12 • 0
0
votes
2
replies
4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.4 years ago by ▴ 80
2
votes
3
replies
3.3k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 15 months ago by 52k • written 15 months ago by • 0
0
votes
3
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971
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
3
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4
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1.3k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
16 months ago Eva ▴ 10
0
votes
3
replies
914
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 18 months ago by 43k • written 18 months ago by • 0
5
votes
7
replies
1.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 18 months ago by 52k • written 18 months ago by ▴ 10
0
votes
3
replies
993
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 19 months ago by 67k • written 19 months ago by • 0
0
votes
3
replies
1.1k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 19 months ago by 67k • written 19 months ago by • 0
1
vote
1
reply
2.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 20 months ago by ★ 4.6k • written 20 months ago by ▴ 10
0
votes
1
reply
1.0k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 20 months ago by 67k • written 20 months ago by • 0
2
votes
2
replies
1.0k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 20 months ago by ★ 4.6k • written 20 months ago by • 0
0
votes
1
reply
869
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
22 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
990
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
5
votes
9
replies
2.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.4 years ago Yang Shi ▴ 10
2
votes
2
replies
1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.4 years ago Yang Shi ▴ 10
0
votes
0
replies
1.1k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.4 years ago eolson • 0
2
votes
2
replies
1.2k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
2
replies
3.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 15 months ago by • 0 • written 2.7 years ago by • 0
3
votes
3
replies
4.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.7 years ago by ▴ 30 • written 5.9 years ago by ▴ 40
5
votes
5
replies
2.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.8 years ago • updated 2.6 years ago 9906201a ▴ 20
1
vote
5
replies
2.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.8 years ago Lucy ▴ 60
1
vote
3
replies
1.7k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
0
votes
1
reply
1.1k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
1
vote
1
reply
3.3k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.3 years ago by ▴ 10 • written 4.5 years ago by ▴ 10
0
votes
5
replies
1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.3 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
1.1k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.4 years ago lianov • 0
0
votes
1
reply
1.2k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.4 years ago • updated 3.3 years ago slcno • 0
3
votes
5
replies
3.3k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 60
0
votes
1
reply
2.3k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
2
votes
3
replies
1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.5 years ago by 52k • written 3.5 years ago by • 0
1
vote
1
reply
2.0k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.5 years ago by ★ 1.1k • written 3.5 years ago by ▴ 20
3
votes
4
replies
1.3k
views
need help regarding differential expression analysis
rna-seq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.6 years ago rbrns • 0
1
vote
4
replies
4.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.6 years ago by ★ 1.1k • written 7.2 years ago by • 0
3
votes
4
replies
1.7k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.6 years ago Antonio M. • 0
1
vote
2
replies
1.3k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.7 years ago by 52k • written 3.7 years ago by ▴ 20
1
vote
7
replies
1.7k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.7 years ago decppced • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Sorry, I didn't see the added response to your original answer. I think that would be a great idea; a novel junction to annot…
Comment: Cannot install GO.db and org.Hs.eg.db by Gabriel • 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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