Showing : rnaseq • reset
2
votes
10
replies
225
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 9 hours ago by 47k • written 4 days ago by • 0
2
votes
2
replies
142
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
23 days ago • updated 13 days ago SciencyUsagi ▴ 10
0
votes
1
reply
136
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 18 days ago by 39k • written 21 days ago by • 0
3
votes
3
replies
153
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 19 days ago by 47k • written 19 days ago by • 0
0
votes
3
replies
170
views
Gene TPM validity with STAR only quantification
RNASeq
updated 20 days ago by • 0 • written 4 weeks ago by ▴ 10
2
votes
5
replies
208
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Create the design matrix
DEGseq edgeR RNASeq
4 weeks ago Mohammad • 0
2
votes
4
replies
284
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
5 weeks ago • updated 4 weeks ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
158
views
DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 5 weeks ago by 39k • written 5 weeks ago by • 0
0
votes
0
replies
82
views
A problem with Experimental Design for Limma
limma RNASeq
6 weeks ago ToReality • 0
0
votes
3
replies
246
views
Unusual MA and volcano plots?
DESeq2 RNASeq
written 7 weeks ago by ▴ 10
0
votes
1
reply
111
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 7 weeks ago by ★ 2.0k
1
vote
2
replies
155
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
93
views
RNA seq analysis
RNASeq
8 weeks ago lesseyl • 0
2
votes
3
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282
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
106
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 8 weeks ago by ★ 2.1k • written 8 weeks ago by • 0
2
votes
4
replies
349
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
176
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 9 weeks ago by 39k • written 11 weeks ago by ▴ 10
1
vote
1
reply
178
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 9 weeks ago by 47k • written 10 weeks ago by • 0
0
votes
3
replies
229
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
1
vote
2
replies
190
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
10 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
123
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 10 weeks ago by ★ 2.1k • written 10 weeks ago by • 0
0
votes
0
replies
95
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
10 weeks ago whduke • 0
0
votes
1
reply
125
views
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
votes
3
replies
154
views
Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 10 weeks ago by 62k • written 10 weeks ago by • 0
0
votes
1
reply
127
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 11 weeks ago by ★ 1.2k • written 11 weeks ago by • 0
2
votes
3
replies
187
views
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
votes
2
replies
210
views
RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 12 weeks ago by 39k • written 3 months ago by • 0
3
votes
7
replies
456
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 12 weeks ago by 47k • written 3 months ago by • 0
1
vote
2
replies
203
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
votes
0
replies
96
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3 months ago rridley3 • 0
3
votes
14
replies
733
views
Atena package - error (new user)
RNAseq R Atena
3 months ago • updated 11 days ago lalanis1 • 0
2
votes
5
replies
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
votes
1
reply
276
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 months ago by 62k • written 3 months ago by • 0
0
votes
0
replies
125
views
question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
4 months ago snowmattin • 0
0
votes
0
replies
122
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
4 months ago Julieta • 0
0
votes
0
replies
124
views
Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
4 months ago estafana.t98 • 0
3
votes
4
replies
311
views
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
170
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
votes
1
reply
209
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 4 months ago by 39k • written 4 months ago by • 0
0
votes
0
replies
129
views
how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
4 months ago marymshahi2021 • 0
0
votes
2
replies
1.4k
views
maSigPro: how to extract the genes in the same cluster
rnaseq
updated 5 months ago by • 0 • written 6.8 years ago by ▴ 10
1
vote
2
replies
234
views
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
votes
1
reply
207
views
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
463
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
updated 5 months ago by ▴ 120 • written 5 months ago by ▴ 10
0
votes
2
replies
409
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 5 months ago by ▴ 220 • written 7 months ago by • 0
0
votes
0
replies
146
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
5 months ago osieman52 • 0
4
votes
5
replies
651
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
175
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
vote
5
replies
500
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 5 months ago by 39k • written 6 months ago by • 0
0
votes
6
replies
532
views
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
Recent ...
Replies
Comment: error in ChAMP loading file by Benth • 0
Shouldn't this p-value, which I presume shows the significance of the fold change, be scale-independent? Additionally, shouldn't all of the…
Comment: AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site) by jeffbrick852 • 0
[us customer service][1] [1]: https://www.us-customer-service.com/
Answer: DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the by swbarnes2 ★ 1.2k
The vignette includes that in the design because the example is a mix of single and paired end reads, and that is added to the design so th…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
`PoolStatus` just indicates whether a sample is a pool or not, i.e., the first option.
Comment: How to map geneIds to ENTREZIDs by stacy.genovese • 0
James - I wish I knew where you lived so I could buy you a beer! Thank you so much for your help. I'm going to work now on converting th…
Votes
A: Limma-voom with external observation weights
Limma-voom with external observation weights
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: How to map geneIds to ENTREZIDs
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