Showing : rnaseq • reset
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 19 months ago by ★ 1.2k • written 2.7 years ago by ▴ 10
1
vote
1
reply
952
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Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
0
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7
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2.3k
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Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
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3
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1.4k
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PCA subset of genes vs DE
DESeq2 RNASeq
written 2.7 years ago by ▴ 20
2
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5
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2.7k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.7 years ago by • 0
0
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3
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1.4k
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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2
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1.7k
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combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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2
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4.6k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 2.8 years ago by • 0
6
votes
11
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2.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.8 years ago mohammedtoufiq91 ▴ 10
2
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1
reply
773
views
EdgeR model matrix
edgeR RNASeq
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
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2.0k
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Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
2
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10
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1.9k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
2
votes
2
replies
787
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
2.9 years ago • updated 2.8 years ago SciencyUsagi ▴ 10
0
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1
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2.9k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
3
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3
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6.9k
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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3
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1.4k
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Gene TPM validity with STAR only quantification
RNASeq
written 2.9 years ago by ▴ 10
2
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5
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1.8k
views
Create the design matrix
DEGseq edgeR RNASeq
2.9 years ago Mohammad • 0
4
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5
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6.4k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 2.8 years ago by 53k • written 2.9 years ago by ▴ 10
0
votes
3
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1.6k
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
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0
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513
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A problem with Experimental Design for Limma
limma RNASeq
2.9 years ago ToReality • 0
0
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3
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2.3k
views
Unusual MA and volcano plots?
DESeq2 RNASeq
written 2.9 years ago by ▴ 10
0
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1
reply
1.1k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.9 years ago by ★ 2.0k
1
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2
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1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
2.9 years ago mohammedtoufiq91 ▴ 10
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0
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552
views
RNA seq analysis
RNASeq
3.0 years ago lesseyl • 0
2
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3
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2.2k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.2k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
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4
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5.8k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
1.2k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
1
vote
1
reply
3.7k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
4
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1.5k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.0 years ago by • 0
1
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2
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1.4k
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
1.5k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
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0
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1.1k
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
3.0 years ago whduke • 0
0
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3
replies
2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 16 months ago by • 0 • written 3.0 years ago by • 0
0
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3
replies
3.2k
views
Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
1
reply
814
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
2
replies
1.3k
views
RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
3
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7
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2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
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2
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1.5k
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
0
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0
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970
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.1 years ago rridley3 • 0
3
votes
16
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3.5k
views
Atena package - error (new user)
RNAseq R Atena
3.1 years ago • updated 2.8 years ago lalanis1 • 0
2
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5
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4.6k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.1 years ago by 43k • written 4.4 years ago by • 0
0
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1
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2.0k
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 3.1 years ago by 68k • written 3.1 years ago by • 0
0
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0
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938
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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
3.2 years ago snowmattin • 0
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0
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1.2k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.2 years ago Julieta • 0
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0
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1.3k
views
Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
3.2 years ago estafana.t98 • 0
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4
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2.5k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
1
reply
1.2k
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by ▴ 30
0
votes
1
reply
925
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1,409 results • Page 4 of 29
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Comment: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by tomaamylikefood • 0
Using biomaRt to extract SNP information from genomic regions is as simple as setting the correct dataset in this case, and defining your …
Comment: Save the Date for EuroBioC2026 in Turku! by tomaamylikefood • 0
If you re interested in staying productive and entertained while following updates from events like EuroBioC2026, you can Download free And…
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I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
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Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Issues with downloading biomaRt - SeqInfo and S4 Vectors
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
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