Showing : RNA-SEQ • reset
5
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
vote
6
replies
865
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 days ago by 42k • written 14 days ago by ▴ 10
0
votes
2
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266
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
7 weeks ago • updated 6 weeks ago paul.meraner • 0
0
votes
0
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181
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
8 weeks ago Fernanda • 0
1
vote
3
replies
543
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 months ago by 67k • written 5 months ago by ▴ 50
2
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4
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646
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 6 months ago by 42k • written 6 months ago by • 0
1
vote
2
replies
591
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
6 months ago Dylan.Sheerin • 0
2
votes
5
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918
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 months ago by ★ 4.5k • written 6 months ago by • 0
3
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3
replies
851
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 51k • written 7 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 11 months ago by ★ 4.5k • written 6.6 years ago by • 0
0
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2
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520
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WGCNA less samples
RNA-Seq WGCNA Worms
12 months ago davca • 0
0
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4
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1.1k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
13 months ago ar14g12 • 0
0
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2
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4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.3 years ago by ▴ 80
2
votes
3
replies
3.2k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 14 months ago by 51k • written 14 months ago by • 0
0
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3
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957
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 14 months ago by ★ 1.9k • written 14 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
15 months ago Eva ▴ 10
0
votes
3
replies
898
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 17 months ago by 42k • written 17 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 51k • written 18 months ago by ▴ 10
0
votes
3
replies
976
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 18 months ago by 67k • written 18 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 18 months ago by 67k • written 18 months ago by • 0
1
vote
1
reply
2.2k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 19 months ago by ★ 4.5k • written 19 months ago by ▴ 10
0
votes
1
reply
970
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 ★ 4.5k • written 20 months ago by • 0
0
votes
1
reply
855
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
21 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
977
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 24 months ago by 42k • written 2.0 years ago by • 0
5
votes
9
replies
2.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.3 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
2.3 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 51k • 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 2.6 years ago by • 0
3
votes
3
replies
3.9k
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 5.8 years ago by ▴ 40
5
votes
5
replies
2.0k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.7 years ago • updated 2.6 years ago 9906201a ▴ 20
1
vote
5
replies
2.5k
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 42k • written 2.8 years ago by • 0
0
votes
5
replies
4.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.5k • 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 51k • 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 4.4 years ago by ▴ 10
0
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5
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1.5k
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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
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0
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1.1k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.3 years ago lianov • 0
0
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1
reply
1.2k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.3 years ago slcno • 0
3
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5
replies
3.2k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 60
0
votes
1
reply
2.2k
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 51k • written 3.5 years ago by • 0
1
vote
1
reply
1.9k
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 3.5 years ago by ★ 4.0k • written 3.5 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
3.5 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
1.6k
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 3.6 years ago by 51k • written 3.7 years ago by ▴ 20
1
vote
7
replies
1.6k
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
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Replies
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
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