Showing : RnaSeq • reset
0
votes
2
replies
355
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
14 days ago • updated 12 days ago sindhuri • 0
0
votes
2
replies
314
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
1
vote
5
replies
559
views
Deseq2 Design
RNASeq DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
0
votes
2
replies
487
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 10
0
votes
1
reply
193
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
votes
5
replies
464
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 9 weeks ago by • 0
0
votes
1
reply
170
views
eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
1
vote
8
replies
1.2k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 weeks ago by • 0
0
votes
0
replies
169
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 weeks ago brayas13 • 0
3
votes
11
replies
827
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
votes
4
replies
474
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
399
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
2
replies
513
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 4 months ago by ▴ 10
0
votes
3
replies
461
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 months ago Travis • 0
0
votes
5
replies
1.8k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.7 years ago by • 0
0
votes
2
replies
969
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
3
votes
5
replies
1.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
2
votes
3
replies
617
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
3
votes
6
replies
866
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 months ago by • 0
4
votes
3
replies
1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 6 months ago by ▴ 10
0
votes
3
replies
616
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
1
vote
4
replies
1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
6 months ago Lucy ▴ 60
0
votes
4
replies
644
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
0
votes
0
replies
386
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
7 months ago JG13 • 0
0
votes
1
reply
408
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 7 months ago by 67k • written 7 months ago by • 0
1
vote
9
replies
1.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
1
vote
3
replies
620
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
2
votes
2
replies
674
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
0
votes
6
replies
1.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
8 months ago • updated 7 months ago atan • 0
3
votes
2
replies
720
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
333
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
10
votes
11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 8 months ago by • 0 • written 7.4 years ago by ▴ 80
1
vote
3
replies
699
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
3
replies
877
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
votes
1
reply
566
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
2
replies
495
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 9 months ago by • 0
0
votes
2
replies
656
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago catv • 0
5
votes
3
replies
1.0k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 9 months ago by • 0
0
votes
1
reply
664
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
1
reply
591
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
0
votes
2
replies
1.2k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
10 months ago kcarey • 0
2
votes
2
replies
564
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
0
votes
2
replies
1.6k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago kcarey • 0
1
vote
4
replies
598
views
DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
vote
3
replies
742
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
0
votes
4
replies
711
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 months ago • updated 10 months ago mperalc • 0
0
votes
2
replies
834
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 months ago by 52k • written 11 months ago by • 0
3
votes
5
replies
1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 11 months ago by ▴ 10
2
votes
1
reply
526
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 months ago by 43k • written 11 months ago by ▴ 10
3
votes
6
replies
1.3k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 months ago boczniak767 ▴ 740
50 results • Page 1 of 1
Recent ...
Replies
Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Joseph Fass ▴ 70
Popular Question to Peter Hickey ▴ 750
Locations • All
United States, 3 minutes ago
India, 4 minutes ago
UPF, Barcelona, Spain, 1 hour ago
United Kingdom, 1 hour ago
France, 2 hours ago
Traffic: 969 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