Showing : RnaSeq • reset
0
votes
0
replies
73
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 days ago JG13 • 0
0
votes
1
reply
162
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 days ago by 66k • written 15 days ago by • 0
1
vote
9
replies
447
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 days ago by 66k • written 21 days ago by • 0
1
vote
3
replies
267
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 21 days ago by 66k • written 21 days ago by ▴ 50
2
votes
2
replies
412
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 4 weeks ago by • 0 • written 6 weeks ago by • 0
0
votes
6
replies
705
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
5 weeks ago atan • 0
2
votes
2
replies
248
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 weeks ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
112
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
6 weeks ago Bibi • 0
10
votes
11
replies
2.0k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 6 weeks ago by • 0 • written 6.9 years ago by ▴ 80
1
vote
3
replies
355
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 weeks ago by 51k • written 7 weeks ago by • 0
0
votes
3
replies
354
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 weeks ago by ★ 4.2k • written 8 weeks ago by • 0
0
votes
1
reply
229
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
0
votes
2
replies
257
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 weeks ago by • 0
0
votes
2
replies
323
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 weeks ago catv • 0
5
votes
3
replies
425
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 weeks ago by 51k • written 10 weeks ago by • 0
0
votes
1
reply
208
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
0
votes
1
reply
204
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 12 weeks ago by ★ 4.2k • written 12 weeks ago by • 0
0
votes
2
replies
426
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
3 months ago kcarey • 0
2
votes
2
replies
340
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
3 months ago Sabiha ▴ 20
0
votes
2
replies
459
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
3 months ago kcarey • 0
1
vote
4
replies
387
views
DESeq2 Replicates
DESeq2 RNASeq
3 months ago kcarey • 0
1
vote
3
replies
456
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 4 months ago by ★ 1.4k • written 4 months ago by ▴ 10
0
votes
4
replies
401
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
4 months ago mperalc • 0
0
votes
2
replies
443
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 4 months ago by 51k • written 4 months ago by • 0
3
votes
5
replies
748
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 4 months ago by 42k • written 4 months ago by ▴ 10
2
votes
1
reply
331
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 4 months ago by 42k • written 4 months ago by ▴ 10
3
votes
6
replies
745
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
4 months ago boczniak767 ▴ 740
0
votes
0
replies
325
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
4 months ago Abril • 0
2
votes
2
replies
568
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
4 months ago jackafiore • 0
1
vote
2
replies
1.3k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 14 months ago by • 0
0
votes
4
replies
506
views
Ballgown error in scan for c.tab files
ballgown RNASeq
5 months ago candacenewcome • 0
1
vote
3
replies
436
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
5 months ago island • 0
1
vote
3
replies
703
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 5 months ago by • 0
0
votes
1
reply
310
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 5 months ago by ▴ 210 • written 5 months ago by • 0
2
votes
4
replies
863
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
5 months ago Sabiha ▴ 20
4
votes
6
replies
751
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 4 months ago by 51k • written 5 months ago by • 0
3
votes
1
reply
395
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
3
replies
669
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 5 months ago by • 0
0
votes
1
reply
332
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
5 months ago WS • 0
2
votes
3
replies
1.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
1
vote
2
replies
562
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
6 months ago Sabiha ▴ 20
1
vote
2
replies
535
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
7 months ago drewhaydensteele • 0
7
votes
2
replies
1.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
3
replies
554
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
7 months ago Karthik • 0
1
vote
1
reply
430
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
2
votes
3
replies
648
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
7 months ago Karthik • 0
2
votes
2
replies
493
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
7 months ago Manthos • 0
2
votes
4
replies
708
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
7 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
490
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
votes
2
replies
620
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 7 months ago by ★ 1.1k • written 8 months ago by ▴ 190
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Awards • All
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to ATpoint ★ 4.2k
Popular Question to WouterDeCoster ▴ 130
Scholar to Gordon Smyth 51k
Voter to Chris ▴ 20
Locations • All
Germany, 4 minutes ago
Wageningen University, Wageningen, the Netherlands, 17 minutes ago
Novartis Institutes for BioMedical Research, 22 minutes ago
United States, 31 minutes ago
France, 39 minutes ago
Traffic: 1140 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