Showing : RNAseq • reset
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 10 days ago by ★ 4.6k • written 10 days ago by • 0
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4
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266
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 7 days ago by ★ 3.4k • written 14 days ago by • 0
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1
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106
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eRNAs count
RNASeq DESeq2
updated 14 days ago by ★ 4.6k • written 14 days ago by • 0
1
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8
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1.0k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 28 days ago by • 0
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0
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130
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
28 days ago brayas13 • 0
3
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11
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713
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 8 weeks ago by • 0
2
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4
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401
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
7 weeks ago jihoon.kim.1495 ▴ 10
1
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1
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270
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
1
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2
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447
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 9 weeks ago by 43k • written 10 weeks ago by ▴ 10
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3
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377
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
9 weeks ago Travis • 0
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5
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1.7k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
0
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2
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884
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
3
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5
replies
938
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
2
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3
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513
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
3 months ago BioinfGuru ▴ 70
3
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6
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800
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
4
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3
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1.2k
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 4 months ago by ▴ 10
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3
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567
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
1
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4
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1.4k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
4 months ago Lucy ▴ 60
0
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4
replies
569
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
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0
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322
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
0
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1
reply
356
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 months ago by 67k • written 5 months ago by • 0
1
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9
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1.4k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 months ago by 67k • written 5 months ago by ▴ 10
1
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3
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552
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 months ago by 67k • written 5 months ago by ▴ 50
2
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2
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620
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 6 months ago by ▴ 10 • written 6 months ago by • 0
0
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6
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1.3k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
6 months ago atan • 0
3
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2
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649
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
0
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0
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286
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
6 months ago Bibi • 0
10
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11
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2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 6 months ago by • 0 • written 7.3 years ago by ▴ 80
1
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3
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634
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 52k • written 6 months ago by • 0
0
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3
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756
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
0
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1
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487
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 months ago by 43k • written 7 months ago by • 0
0
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2
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442
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 7 months ago by • 0
0
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2
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579
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 months ago catv • 0
5
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3
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861
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 52k • written 7 months ago by • 0
0
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1
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565
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 months ago by 43k • written 7 months ago by • 0
0
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1
reply
488
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
0
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2
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1.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 months ago kcarey • 0
2
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2
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519
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
0
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2
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1.2k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 months ago kcarey • 0
1
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4
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552
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DESeq2 Replicates
DESeq2 RNASeq
9 months ago kcarey • 0
1
vote
3
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663
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
0
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4
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661
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 months ago mperalc • 0
0
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2
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742
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 months ago by 52k • written 9 months ago by • 0
3
votes
5
replies
1.1k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
2
votes
1
reply
490
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
3
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6
replies
1.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
9 months ago boczniak767 ▴ 740
0
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0
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501
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
2
votes
2
replies
999
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 months ago • updated 9 months ago jackafiore • 0
1
vote
2
replies
1.8k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 19 months ago by • 0
0
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4
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707
views
Ballgown error in scan for c.tab files
ballgown RNASeq
10 months ago candacenewcome • 0
50 results • Page 1 of 1
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Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
Yes, I did. Here is my code. data.path <- "~/GeoMx_best_practice/data/" filepath <- paste(data.path, "Joon_QC_NPC_4_…
Comment: fail to use addPerROIQC in Rmd by shepherl 4.1k
Just covering all bases. You defined spe earlier in the R markdown that is not shown?
Comment: Open Sesame: in what genes are my differentially methylated probes!! by alyssa-daniel • 0
@zhouwanding I have a question regarding DML analysis. I understand the Est_ output is describing the difference in methylation between the…
Comment: DESeq2 dispersion estimates fitting drastically different based on explanatory v by Sam • 0
Here is the explanatory variables![enter image description here][1] uses if that helps address the problem as well [1]: /media/images/…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
Thanks, @gabrielhoffman My understanding is that both options would still be mixed models: Even with technical replicates (3 wells per d…
Votes
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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