Showing : RNASEQ • reset
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
11 days ago • updated 9 days ago sindhuri • 0
0
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2
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306
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
1
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5
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555
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Deseq2 Design
RNASeq DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
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2
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483
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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
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1
reply
190
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
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5
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458
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 9 weeks ago by • 0
0
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1
reply
167
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eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
1
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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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165
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 weeks ago brayas13 • 0
3
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11
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818
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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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471
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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
389
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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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511
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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3
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455
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 months ago Travis • 0
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
0
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2
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962
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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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1.2k
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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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609
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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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861
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 5 months ago by • 0
4
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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
0
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3
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614
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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
0
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4
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636
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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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379
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 months ago JG13 • 0
0
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1
reply
404
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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
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
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3
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617
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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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
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6
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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
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2
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713
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
0
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0
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327
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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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696
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
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3
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868
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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
reply
564
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
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2
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490
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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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653
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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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993
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
655
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
reply
585
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
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
10 months ago kcarey • 0
2
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2
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561
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
0
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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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595
views
DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
vote
3
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737
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
0
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4
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709
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
0
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2
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832
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
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
522
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
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Replies
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
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
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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