Showing : RNAseq • reset
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3
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143
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
2 days ago • updated 1 day ago Travis • 0
1
vote
1
reply
125
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
4 days ago • updated 8 hours ago Ben ▴ 10
0
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5
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1.5k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.4 years ago by • 0
0
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2
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742
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 28 days ago by ★ 1.4k • written 29 days ago by • 0
3
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5
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694
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
2
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3
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352
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 weeks ago BioinfGuru ▴ 70
3
votes
6
replies
693
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 weeks ago by • 0
4
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3
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1.1k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 10 weeks ago by ▴ 10
0
votes
3
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472
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 9 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
1
vote
4
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1.2k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
11 weeks ago • updated 9 weeks ago Lucy ▴ 60
0
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4
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443
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 11 weeks ago by • 0
0
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0
replies
233
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
3 months ago JG13 • 0
0
votes
1
reply
296
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
9
replies
967
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 3 months ago by 67k • written 3 months ago by ▴ 10
1
vote
3
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450
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
2
votes
2
replies
554
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 3 months ago by ▴ 10 • written 4 months ago by • 0
0
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6
replies
1.0k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
4 months ago atan • 0
3
votes
2
replies
500
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
4 months ago mohammedtoufiq91 ▴ 10
0
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0
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230
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
4 months ago Bibi • 0
10
votes
11
replies
2.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 months ago by • 0 • written 7.1 years ago by ▴ 80
1
vote
3
replies
535
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
0
votes
3
replies
584
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 months ago by ★ 4.4k • written 4 months ago by • 0
0
votes
1
reply
369
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 months ago by 42k • written 5 months ago by • 0
0
votes
2
replies
380
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 5 months ago by • 0
0
votes
2
replies
478
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 months ago catv • 0
5
votes
3
replies
653
views
Log-cpm values from limma
limma edgeR RNASeq
updated 4 months ago by 51k • written 5 months ago by • 0
0
votes
1
reply
421
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 months ago by 42k • written 5 months ago by • 0
0
votes
1
reply
362
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
0
votes
2
replies
761
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 months ago kcarey • 0
2
votes
2
replies
446
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 months ago Sabiha ▴ 20
0
votes
2
replies
834
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 months ago kcarey • 0
1
vote
4
replies
484
views
DESeq2 Replicates
DESeq2 RNASeq
6 months ago kcarey • 0
1
vote
3
replies
578
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 months ago by ★ 1.4k • written 7 months ago by ▴ 10
0
votes
4
replies
579
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 months ago mperalc • 0
0
votes
2
replies
643
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 months ago by 51k • written 7 months ago by • 0
3
votes
5
replies
928
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 months ago by 42k • written 7 months ago by ▴ 10
2
votes
1
reply
431
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 months ago by 42k • written 7 months ago by ▴ 10
3
votes
6
replies
987
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
7 months ago boczniak767 ▴ 740
0
votes
0
replies
444
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
7 months ago Abril • 0
2
votes
2
replies
819
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
7 months ago jackafiore • 0
1
vote
2
replies
1.6k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 17 months ago by • 0
0
votes
4
replies
628
views
Ballgown error in scan for c.tab files
ballgown RNASeq
8 months ago • updated 7 months ago candacenewcome • 0
1
vote
3
replies
593
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
8 months ago island • 0
1
vote
3
replies
882
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 8 months ago by • 0
0
votes
1
reply
418
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 8 months ago by ▴ 210 • written 8 months ago by • 0
2
votes
4
replies
1.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
8 months ago Sabiha ▴ 20
4
votes
6
replies
939
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 7 months ago by 51k • written 8 months ago by • 0
3
votes
1
reply
525
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 8 months ago by 51k • written 8 months ago by • 0
0
votes
3
replies
907
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 8 months ago by • 0
0
votes
1
reply
458
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
8 months ago WS • 0
50 results • Page 1 of 1
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Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Comment: ISO a solution to rank-order introns by transcript by James W. MacDonald 67k
There's an error in the last line. Note that `sapply(lengths(z), seq_len)` will return a `list` because the lengths vary. We need a vector,…
Comment: BiomaRt - improved access to Ensembl ? by Mike Smith ★ 6.5k
Why do you want to use `useMart()` rather than `useEnsembl()`? They are essentially the same (`useEnsembl()` will eventually call `useMart(…
Comment: Installing Bioconductor packages in Docker by devarti.mahakalkar • 0
I have installed BiocManager on my base image rather than having it as base image. RUN Rscript -e "install.packages('BiocManager', re…
Comment: Meta-analysis on RNA-seq data sets by Travis • 0
Thank you for your suggestions and explanation of your approach!
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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