Showing : RNAseq • reset
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 17 months ago by ★ 1.2k • written 2.6 years ago by ▴ 10
1
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1
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936
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Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 20
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7
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2.2k
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Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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2
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1.3k
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PCA subset of genes vs DE
DESeq2 RNASeq
2.6 years ago andrebolerbarros ▴ 20
2
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5
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2.6k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.6 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 2.6 years ago by 53k • written 2.6 years ago by • 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 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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2
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4.6k
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Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 2.7 years ago by • 0
6
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11
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2.3k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago • updated 2.6 years ago mohammedtoufiq91 ▴ 10
2
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1
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748
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EdgeR model matrix
edgeR RNASeq
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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2.0k
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Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
2
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10
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1.8k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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2
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755
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Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
2.8 years ago • updated 2.7 years ago SciencyUsagi ▴ 10
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1
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2.9k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
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3
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
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3
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1.3k
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Gene TPM validity with STAR only quantification
RNASeq
written 2.8 years ago by ▴ 10
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5
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1.8k
views
Create the design matrix
DEGseq edgeR RNASeq
2.8 years ago Mohammad • 0
4
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5
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6.3k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 2.7 years ago by 53k • written 2.8 years ago by ▴ 10
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3
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1.5k
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
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0
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495
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A problem with Experimental Design for Limma
limma RNASeq
2.8 years ago ToReality • 0
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3
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2.3k
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Unusual MA and volcano plots?
DESeq2 RNASeq
written 2.8 years ago by ▴ 10
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1
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1.1k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.8 years ago by ★ 2.0k
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2
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1.2k
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
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0
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542
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RNA seq analysis
RNASeq
2.9 years ago lesseyl • 0
2
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3
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2.1k
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.9 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
1.1k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
2
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4
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5.7k
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
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1
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1.1k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 10
1
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1
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3.7k
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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4
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1.3k
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Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 2.9 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
2.9 years ago mohammedtoufiq91 ▴ 10
0
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1
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1.5k
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Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
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0
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1.0k
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.9 years ago whduke • 0
0
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3
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2.3k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 15 months ago by • 0 • written 2.9 years ago by • 0
0
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3
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3.2k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
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1
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799
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Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by • 0
2
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3
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2.3k
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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2
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1.2k
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RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 2.9 years ago by 43k • written 3.0 years ago by • 0
3
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7
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2.8k
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
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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 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
0
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0
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911
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.0 years ago rridley3 • 0
3
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16
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3.5k
views
Atena package - error (new user)
RNAseq R Atena
3.0 years ago • updated 2.7 years ago lalanis1 • 0
2
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5
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4.5k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.0 years ago by 43k • written 4.3 years ago by • 0
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1
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1.9k
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Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
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0
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901
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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
3.0 years ago snowmattin • 0
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0
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1.1k
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.0 years ago Julieta • 0
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0
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1.3k
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Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
3.1 years ago estafana.t98 • 0
3
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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 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
1
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1
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1.2k
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 30
0
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1
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904
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1,409 results • Page 4 of 29
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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