Showing : RnaSeq • reset
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
15 days ago • updated 13 days ago sindhuri • 0
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2
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316
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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5
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560
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Deseq2 Design
RNASeq DESeq2
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
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2
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488
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 6 weeks ago by 52k • written 7 weeks ago by ▴ 10
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1
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197
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
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5
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474
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 9 weeks ago by • 0
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1
reply
171
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eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
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8
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1.2k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 weeks ago by • 0
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0
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170
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 weeks ago brayas13 • 0
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11
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838
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
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4
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475
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
407
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
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2
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516
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 4 months ago by ▴ 10
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3
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469
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
4 months ago Travis • 0
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5
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1.8k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.7 years ago by • 0
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2
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974
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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
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5
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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
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3
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624
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
3
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6
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871
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 months ago by • 0
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3
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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
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3
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617
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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
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4
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1.5k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
6 months ago Lucy ▴ 60
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4
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646
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
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0
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390
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
7 months ago JG13 • 0
0
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410
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 7 months ago by 67k • written 7 months ago by • 0
1
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9
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1.7k
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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
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3
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623
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
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2
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680
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
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6
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1.4k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
8 months ago atan • 0
3
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2
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723
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
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337
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
10
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11
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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
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3
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701
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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
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3
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879
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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
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1
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571
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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
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2
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497
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 9 months ago by • 0
0
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2
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661
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago catv • 0
5
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3
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1.0k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 9 months ago by • 0
0
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1
reply
670
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
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1
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594
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
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2
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1.2k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
10 months ago kcarey • 0
2
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2
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568
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
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2
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1.6k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago kcarey • 0
1
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4
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602
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DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
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3
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745
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
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4
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712
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 months ago mperalc • 0
0
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2
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837
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 months ago by 52k • written 11 months ago by • 0
3
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5
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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
528
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 months ago by 43k • written 11 months ago by ▴ 10
3
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6
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1.3k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 months ago boczniak767 ▴ 740
50 results • Page 1 of 1
Recent ...
Replies
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
Votes
Comment: Recount3 data correspond to TCGA data
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
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