Showing : rnaseq • reset
0
votes
2
replies
338
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
10 days ago • updated 8 days ago sindhuri • 0
0
votes
2
replies
303
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
1
vote
5
replies
553
views
Deseq2 Design
RNASeq DESeq2
updated 4 weeks ago by 67k • written 5 weeks ago by • 0
0
votes
2
replies
483
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
190
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
456
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 8 weeks ago by • 0
0
votes
1
reply
166
views
eRNAs count
RNASeq DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 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 10 weeks ago by • 0
0
votes
0
replies
164
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
10 weeks ago brayas13 • 0
3
votes
11
replies
812
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
votes
4
replies
468
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
386
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
2
replies
507
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
votes
3
replies
454
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
957
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
1.1k
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
604
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
3
votes
6
replies
858
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 5 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
613
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ★ 4.6k • written 5 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
632
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
378
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 months ago JG13 • 0
0
votes
1
reply
404
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
613
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
669
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
712
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
326
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
695
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
864
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
561
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
2
replies
487
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
650
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago catv • 0
5
votes
3
replies
985
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
651
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
582
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
560
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
1.5k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago kcarey • 0
1
vote
4
replies
592
views
DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
vote
3
replies
732
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
0
votes
4
replies
708
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
0
votes
2
replies
829
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 months ago by 52k • written 10 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
521
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
3
votes
6
replies
1.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 months ago boczniak767 ▴ 740
50 results • Page 1 of 1
Recent ...
Replies
Answer: Curiously shaped volcano plot with using oarfish + swish to do differential gene by Michael Love 43k
See swish vignette, these are explained.
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to Bob ▴ 10
Popular Question to shepherl 4.1k
Scholar to James W. MacDonald 67k
Popular Question to Assa Yeroslaviz ★ 1.5k
Locations • All
The city by the bay, 24 minutes ago
Pakistan, 2 hours ago
Portugal, 4 hours ago
United States, 5 hours ago
United Kingdom, 6 hours ago
Traffic: 463 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