Showing : RNA-Seq • reset
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 13 months ago by 53k • written 13 months ago by ▴ 80
1
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6
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1.8k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 16 months ago by 43k • written 16 months ago by ▴ 10
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2
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782
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
17 months ago paul.meraner • 0
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0
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691
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
17 months ago Fernanda • 0
1
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3
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1.2k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 21 months ago by 68k • written 21 months ago by ▴ 50
2
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4
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1.2k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 22 months ago by 43k • written 22 months ago by • 0
1
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2
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1.2k
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
22 months ago Dylan.Sheerin • 0
2
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6
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3.1k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 months ago by • 0 • written 22 months ago by • 0
3
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3
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2.1k
views
permutation test in edgeR
rna-seq edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
0
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2
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901
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WGCNA less samples
RNA-Seq WGCNA Worms
2.3 years ago davca • 0
0
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4
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1.6k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.4 years ago ar14g12 • 0
2
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3
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5.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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3
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1.5k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by • 0
3
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4
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2.8k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.6 years ago Eva ▴ 30
0
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3
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1.5k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
5
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7
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2.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
0
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3
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1.4k
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 2.8 years ago by 68k • written 2.8 years ago by • 0
0
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3
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1.6k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
1
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1
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3.5k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
0
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1
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1.9k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
2
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2
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1.4k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
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1
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1.2k
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
3.1 years ago Jenny Drnevich ★ 2.0k
0
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1
reply
1.4k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
5
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9
replies
3.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
3.6 years ago Yang Shi ▴ 10
2
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2
replies
2.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.6 years ago Yang Shi ▴ 10
0
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0
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1.3k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
3.7 years ago eolson • 0
2
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2
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1.9k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
0
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2
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4.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.5 years ago by • 0 • written 3.9 years ago by • 0
5
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5
replies
3.4k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
4.0 years ago • updated 3.9 years ago 9906201a ▴ 20
1
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5
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3.7k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
4.1 years ago Lucy ▴ 60
1
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3
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2.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
reply
1.5k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
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5
replies
2.2k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.6 years ago bioinformatic_trainee ▴ 10
0
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0
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1.5k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.6 years ago lianov • 0
0
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1
reply
1.6k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.6 years ago slcno • 0
3
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5
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6.1k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 60
0
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1
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3.4k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
2
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3
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1.9k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.8 years ago by 53k • written 4.8 years ago by • 0
1
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1
reply
2.5k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.8 years ago by ★ 1.1k • written 4.8 years ago by ▴ 20
3
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4
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1.7k
views
need help regarding differential expression analysis
rna-seq
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 20
0
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0
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1.5k
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
4.8 years ago rbrns • 0
3
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4
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2.1k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.9 years ago Antonio M. • 0
1
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2
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1.7k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 4.9 years ago by 53k • written 5.0 years ago by ▴ 20
0
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5
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6.7k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.2 years ago by ★ 5.0k • written 5.0 years ago by • 0
1
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7
replies
2.2k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
5.0 years ago decppced • 0
1
vote
3
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1.3k
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
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0
replies
1.3k
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
5.1 years ago wrzl • 0
0
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1
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1.7k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
3
votes
9
replies
3.6k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
5.3 years ago • updated 5.2 years ago Pufall, Miles A ▴ 30
0
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2
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2.7k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 70
418 results • Page 1 of 9
Recent ...
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Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
Votes
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
Answer: Quick two questions on limpa
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