Showing : RNAseq • reset
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
20 hours ago • updated 1 hour ago k.roelfs • 0
2
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2
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139
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Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
19 days ago • updated 9 days ago SciencyUsagi ▴ 10
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1
reply
119
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 14 days ago by 39k • written 17 days ago by • 0
3
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3
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143
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 15 days ago by 47k • written 15 days ago by • 0
0
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3
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150
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Gene TPM validity with STAR only quantification
RNASeq
updated 16 days ago by • 0 • written 27 days ago by ▴ 10
2
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5
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198
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Create the design matrix
DEGseq edgeR RNASeq
29 days ago • updated 28 days ago Mohammad • 0
2
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4
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280
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How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
4 weeks ago mohammedtoufiq91 ▴ 10
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3
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153
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 4 weeks ago by 39k • written 5 weeks ago by • 0
0
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0
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81
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A problem with Experimental Design for Limma
limma RNASeq
6 weeks ago ToReality • 0
0
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3
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240
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Unusual MA and volcano plots?
DESeq2 RNASeq
written 6 weeks ago by ▴ 10
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1
reply
109
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 6 weeks ago by ★ 2.0k
1
vote
2
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152
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
7 weeks ago mohammedtoufiq91 ▴ 10
0
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0
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92
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RNA seq analysis
RNASeq
7 weeks ago lesseyl • 0
2
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3
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262
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
8 weeks ago • updated 7 weeks ago mohammedtoufiq91 ▴ 10
0
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1
reply
98
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 8 weeks ago by ★ 2.1k • written 8 weeks ago by • 0
2
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4
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328
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
8 weeks ago mohammedtoufiq91 ▴ 10
0
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1
reply
165
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Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 8 weeks ago by 39k • written 11 weeks ago by ▴ 10
1
vote
1
reply
169
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 8 weeks ago by 47k • written 9 weeks ago by • 0
0
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3
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226
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Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
1
vote
2
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187
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
9 weeks ago mohammedtoufiq91 ▴ 10
0
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1
reply
118
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Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 9 weeks ago by ★ 2.1k • written 9 weeks ago by • 0
0
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0
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90
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
10 weeks ago whduke • 0
0
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1
reply
122
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
0
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3
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142
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 10 weeks ago by 62k • written 10 weeks ago by • 0
0
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1
reply
126
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Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 10 weeks ago by ★ 1.2k • written 11 weeks ago by • 0
2
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3
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183
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 11 weeks ago by 47k • written 11 weeks ago by • 0
0
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2
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206
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RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 12 weeks ago by 39k • written 3 months ago by • 0
3
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7
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450
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 12 weeks ago by 47k • written 12 weeks ago by • 0
1
vote
2
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201
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
0
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0
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94
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3 months ago rridley3 • 0
3
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14
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722
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Atena package - error (new user)
RNAseq R Atena
3 months ago • updated 7 days ago lalanis1 • 0
2
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5
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1.5k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3 months ago by 39k • written 19 months ago by • 0
0
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1
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275
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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 months ago by 62k • written 3 months ago by • 0
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0
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121
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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
4 months ago snowmattin • 0
0
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0
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119
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
4 months ago Julieta • 0
0
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0
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124
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Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
4 months ago estafana.t98 • 0
3
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4
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308
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difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
0
votes
1
reply
167
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
0
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1
reply
208
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 4 months ago by 39k • written 4 months ago by • 0
0
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0
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128
views
how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
4 months ago marymshahi2021 • 0
0
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2
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1.4k
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maSigPro: how to extract the genes in the same cluster
rnaseq
updated 4 months ago by • 0 • written 6.8 years ago by ▴ 10
1
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2
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233
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how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 5 months ago by ★ 2.1k • written 5 months ago by • 0
0
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1
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196
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Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 5 months ago by 39k • written 5 months ago by • 0
2
votes
7
replies
458
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
updated 5 months ago by ▴ 120 • written 5 months ago by ▴ 10
0
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2
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406
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 5 months ago by ▴ 220 • written 7 months ago by • 0
0
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0
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140
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
5 months ago osieman52 • 0
4
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5
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643
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 5 months ago by 39k • written 5 months ago by • 0
1
vote
1
reply
174
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 5 months ago by ★ 2.1k • written 5 months ago by • 0
1
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5
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493
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 5 months ago by 39k • written 5 months ago by • 0
0
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6
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528
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
6 months ago • updated 5 months ago Weiqian • 0
50 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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