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Showing :
RNASeq
•
reset
3
votes
6
replies
520
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 15 days ago by
Ahmed Salah
• 0
0
votes
2
replies
405
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 5 days ago by
MarcHintz99
• 0 • written 11 weeks ago by
Rui
• 0
0
votes
1
reply
203
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 8 weeks ago by
Gordon Smyth
53k • written 9 weeks ago by
ilaria.massaiu
• 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 10 weeks ago by
Gordon Smyth
53k • written 12 weeks ago by
abaed
• 0
0
votes
1
reply
3.2k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 11.1 years ago by
gcyuan
• 0
2
votes
9
replies
955
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq
edgeR
LongRead
Transcript
3 months ago
mohammedtoufiq91
▴ 10
0
votes
8
replies
627
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
4 months ago • updated 3 months ago
Jiahao Tian
• 0
3
votes
13
replies
2.2k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 14 months ago by
bioshot.com
• 0
3
votes
2
replies
887
views
Transcript expression analysis using EdgeR
edgeR
Transcript
RNASeq
4 months ago
mohammedtoufiq91
▴ 10
0
votes
5
replies
888
views
WGCNA
WGCNA
Normalization
RNASeq
written 9 months ago by
Vishnu
• 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 6 months ago by
Christian
▴ 20
0
votes
1
reply
573
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 6 months ago by
Michael Love
43k • written 6 months ago by
s.malik
• 0
2
votes
5
replies
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps
RNASeq
updated 6 months ago by
Paul Harrison
▴ 110 • written 6 months ago by
giovanna
▴ 10
0
votes
0
replies
311
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
6 months ago
dudwnsrla1
• 0
4
votes
7
replies
3.3k
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
7 months ago • updated 8 weeks ago
massimo
▴ 10
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
Shaimaa Gamal
• 0
0
votes
4
replies
1.2k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 8 months ago by
questionanswer
• 0
0
votes
0
replies
465
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
8 months ago
GT
• 0
0
votes
3
replies
1000
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Marwan
• 0
1
vote
2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
ingrid.h
• 0
0
votes
1
reply
407
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 9 months ago by
Michael Love
43k • written 10 months ago by
Sahil
• 0
0
votes
3
replies
866
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 10 months ago by
jodan
• 0 • written 10 months ago by
Quang NN
▴ 10
0
votes
1
reply
646
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Sim
• 0
0
votes
2
replies
904
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
10 months ago • updated 9 months ago
ingrid.h
• 0
0
votes
4
replies
1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
10 months ago
Quang NN
▴ 10
0
votes
3
replies
912
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 11 months ago by
sindhuri
• 0
4
votes
2
replies
999
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
bbao
▴ 10
1
vote
5
replies
1.0k
views
Deseq2 Design
RNASeq
DESeq2
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
pm_25
• 0
0
votes
2
replies
925
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 12 months ago by
Gordon Smyth
53k • written 12 months ago by
Lina
▴ 10
0
votes
1
reply
703
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
siobhan.dietz
• 0
1
vote
5
replies
1.2k
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 12 months ago by
Kent
• 0
0
votes
1
reply
423
views
eRNAs count
RNASeq
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Irene
• 0
1
vote
8
replies
2.5k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 13 months ago by
Adam Marstrand
• 0
0
votes
0
replies
397
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
13 months ago
brayas13
• 0
2
votes
4
replies
908
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
14 months ago
jihoon.kim.1495
▴ 10
1
vote
1
reply
1.0k
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Caroline
• 0
1
vote
2
replies
894
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Ben
▴ 10
0
votes
3
replies
1.1k
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
14 months ago
Travis
• 0
0
votes
5
replies
2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 4.6 years ago by
jehimi
• 0
0
votes
2
replies
1.6k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Shwetal
• 0
3
votes
5
replies
2.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2
RNAseq
DifferentialExpression
updated 16 months ago by
swbarnes2
★ 1.4k • written 16 months ago by
BioNovice247
• 0
2
votes
3
replies
1.3k
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
16 months ago • updated 15 months ago
BioinfGuru
▴ 70
3
votes
6
replies
1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 16 months ago by
MedocRafael
• 0
4
votes
3
replies
1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
written 16 months ago by
mila
▴ 10
0
votes
3
replies
996
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 16 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Mark
• 0
1
vote
4
replies
2.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
17 months ago • updated 16 months ago
Lucy
▴ 60
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 17 months ago by
Shaozhen
• 0
0
votes
0
replies
715
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
17 months ago
JG13
• 0
0
votes
1
reply
725
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
cbio
• 0
1
vote
9
replies
3.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 17 months ago by
James W. MacDonald
68k • written 18 months ago by
adrip
▴ 10
1,410 results • Page
1 of 29
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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