Showing : rnaseq • reset
0
votes
0
replies
7
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
18 minutes ago cbio • 0
1
vote
9
replies
280
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 19 hours ago by 66k • written 5 days ago by • 0
1
vote
3
replies
186
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 days ago by 66k • written 6 days ago by ▴ 50
2
votes
2
replies
379
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 14 days ago by • 0 • written 29 days ago by • 0
0
votes
6
replies
651
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
25 days ago • updated 19 days ago atan • 0
2
votes
2
replies
219
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
27 days ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
96
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
4 weeks ago Bibi • 0
10
votes
11
replies
2.0k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 27 days ago by • 0 • written 6.8 years ago by ▴ 80
1
vote
3
replies
338
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 weeks ago by 51k • written 5 weeks ago by • 0
0
votes
3
replies
312
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
votes
1
reply
204
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
votes
2
replies
230
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 8 weeks ago by • 0
0
votes
2
replies
296
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 weeks ago catv • 0
5
votes
3
replies
385
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 weeks ago by 51k • written 8 weeks ago by • 0
0
votes
1
reply
179
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
votes
1
reply
188
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 weeks ago by ★ 4.2k • written 10 weeks ago by • 0
0
votes
2
replies
374
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
12 weeks ago kcarey • 0
2
votes
2
replies
326
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
420
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
3 months ago kcarey • 0
1
vote
4
replies
371
views
DESeq2 Replicates
DESeq2 RNASeq
3 months ago kcarey • 0
1
vote
3
replies
444
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 3 months ago by ★ 1.4k • written 3 months ago by ▴ 10
0
votes
4
replies
380
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
3 months ago mperalc • 0
0
votes
2
replies
415
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 51k • written 3 months ago by • 0
3
votes
5
replies
724
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
2
votes
1
reply
317
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
votes
6
replies
701
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
4 months ago • updated 3 months ago boczniak767 ▴ 740
0
votes
0
replies
300
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
4 months ago Abril • 0
2
votes
2
replies
532
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 13 months ago by • 0
0
votes
4
replies
492
views
Ballgown error in scan for c.tab files
ballgown RNASeq
4 months ago candacenewcome • 0
1
vote
3
replies
411
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
4 months ago island • 0
1
vote
3
replies
673
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
299
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 4 months ago by ▴ 210 • written 4 months ago by • 0
2
votes
4
replies
799
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
6
replies
721
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
375
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
3
replies
639
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 5 months ago by • 0
0
votes
1
reply
316
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
5 months ago WS • 0
2
votes
3
replies
1.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 6 months ago by • 0
1
vote
2
replies
539
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
6 months ago • updated 5 months ago Sabiha ▴ 20
1
vote
2
replies
511
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
6 months ago drewhaydensteele • 0
7
votes
2
replies
1000
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
3
replies
541
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago Karthik • 0
1
vote
1
reply
422
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
2
votes
3
replies
610
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
6 months ago Karthik • 0
2
votes
2
replies
478
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 • updated 6 months ago Manthos • 0
2
votes
4
replies
694
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
7 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
482
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
600
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 7 months ago by ★ 1.1k • written 7 months ago by ▴ 190
0
votes
9
replies
2.6k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 7 months ago by • 0 • written 6.6 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: Combining two bulk RNA seq datasets by Tanvi • 0
Thank you for your suggestion. However, my R version on server is 4.1.1 and BatchQC requires R version more than 4.3, but I created PCA plo…
Comment: Create multiple DoparParams with different number of registered cores by ATpoint ★ 4.2k
https://github.com/Bioconductor/BiocParallel/blob/devel/R/DoparParam-class.R DoparParam is a BiocParallel class, that is why I am asking …
Answer: Combining two bulk RNA seq datasets by W. Evan Johnson ▴ 850
Hello, I would recommend you use BatchQC (bioconductor package) to evaluate the extent to which batch effects impact your data. Not all bat…
Comment: Create multiple DoparParams with different number of registered cores by James W. MacDonald 66k
`registerDoParallel` and `DoparParam` are both `doParallel` functions, which again, is a CRAN package. What part of the code you present ab…
Answer: Create multiple DoparParams with different number of registered cores by Martin Morgan 25k
I think the answer is "you can't". `DoparParam()` provides a 'wrapper' around doParallel functionality, e.g., `bpworkers(DoparParam())` rea…
Votes
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
Awards • All
Popular Question to maltethodberg ▴ 180
Popular Question to W. Evan Johnson ▴ 850
Popular Question to Michael Love 42k
Popular Question to rae.alshammari ▴ 10
Popular Question to Alejandro Reyes ★ 1.9k
Locations • All
Spain, 4 minutes ago
United States, 5 minutes ago
Switzerland, 8 minutes ago
Slovakia, 11 minutes ago
Italy, 15 minutes ago
Traffic: 736 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