Showing : RNASEQ • reset
5
votes
7
replies
1.8k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 2.1 years ago by 53k • written 2.9 years ago by • 0
0
votes
2
replies
1.7k
views
GO analysis in R vs website
GO RNASeq
2.9 years ago Nitro • 0
1
vote
4
replies
1.5k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.9 years ago DH • 0
1
vote
0
replies
1.3k
views
Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
2.9 years ago Jamie Walters ▴ 10
3
votes
2
replies
1.6k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.9 years ago chf • 0
1
vote
3
replies
2.0k
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 21 months ago by ★ 1.2k • written 2.9 years ago by ▴ 10
1
vote
1
reply
992
views
Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 20
0
votes
7
replies
2.5k
views
Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
3
replies
1.5k
views
PCA subset of genes vs DE
DESeq2 RNASeq
written 2.9 years ago by ▴ 20
2
votes
5
replies
2.8k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.9 years ago by • 0
0
votes
3
replies
1.5k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
2
replies
1.8k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
2
replies
4.9k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 3.0 years ago by • 0
6
votes
11
replies
2.5k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
811
views
EdgeR model matrix
edgeR RNASeq
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
2
replies
2.2k
views
Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
10
replies
2.0k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
votes
2
replies
825
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
3.1 years ago SciencyUsagi ▴ 10
0
votes
1
reply
3.2k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
3
votes
3
replies
7.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
3
replies
1.5k
views
Gene TPM validity with STAR only quantification
RNASeq
written 3.1 years ago by ▴ 10
2
votes
5
replies
1.9k
views
Create the design matrix
DEGseq edgeR RNASeq
3.1 years ago Mohammad • 0
4
votes
5
replies
6.9k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 3.0 years ago by 53k • written 3.1 years ago by ▴ 10
0
votes
3
replies
1.7k
views
DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
0
replies
554
views
A problem with Experimental Design for Limma
limma RNASeq
3.1 years ago ToReality • 0
0
votes
3
replies
2.5k
views
Unusual MA and volcano plots?
DESeq2 RNASeq
written 3.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 3.2 years ago by ★ 2.0k
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
574
views
RNA seq analysis
RNASeq
3.2 years ago lesseyl • 0
2
votes
3
replies
2.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.3k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
2
votes
4
replies
6.2k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.3k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
1
vote
1
reply
4.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
4
replies
1.6k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.2 years ago by • 0
1
vote
2
replies
1.6k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
votes
0
replies
1.1k
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
3.2 years ago whduke • 0
0
votes
3
replies
2.6k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 months ago by • 0 • written 3.2 years ago by • 0
0
votes
3
replies
3.4k
views
Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
1
reply
834
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
2
votes
3
replies
2.5k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
2
replies
1.4k
views
RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
3
votes
7
replies
3.0k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
vote
2
replies
1.6k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
0
votes
0
replies
1.1k
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.3 years ago rridley3 • 0
3
votes
16
replies
3.7k
views
Atena package - error (new user)
RNAseq R Atena
3.3 years ago • updated 3.0 years ago lalanis1 • 0
2
votes
5
replies
4.7k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.3 years ago by 43k • written 4.6 years ago by • 0
0
votes
1
reply
2.1k
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
0
replies
988
views
question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
3.4 years ago snowmattin • 0
1,413 results • Page 4 of 29
Recent ...
Replies
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Votes
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Awards • All
Teacher to Michael Love 43k
Supporter to fl ▴ 20
Popular Question to James W. MacDonald 68k
Popular Question to rcavalca ▴ 140
Popular Question to James Aiden • 0
Locations • All
United Kingdom, 29 minutes ago
USA, 32 minutes ago
United States, 45 minutes ago
United States, 53 minutes ago
United States, 56 minutes ago
Traffic: 1974 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