Showing : RnaSeq • reset
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82
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 5 days ago by ★ 4.5k • written 5 days ago by • 0
0
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4
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246
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 2 days ago by ★ 3.4k • written 9 days ago by • 0
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1
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92
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eRNAs count
RNASeq DESeq2
updated 9 days ago by ★ 4.5k • written 9 days ago by • 0
1
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8
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997
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 23 days ago by • 0
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0
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129
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
23 days ago brayas13 • 0
3
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11
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705
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 7 weeks ago by • 0
2
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4
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392
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
7 weeks ago jihoon.kim.1495 ▴ 10
1
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1
reply
262
views
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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436
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 8 weeks ago by 43k • written 9 weeks ago by ▴ 10
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3
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376
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
9 weeks ago • updated 8 weeks ago Travis • 0
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5
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1.7k
views
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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877
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 12 weeks ago by ★ 1.4k • written 3 months ago by • 0
3
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5
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927
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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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499
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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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794
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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
0
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3
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559
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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 ★ 4.5k • written 4 months ago by • 0
1
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4
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1.4k
views
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
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560
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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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317
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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
354
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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546
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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617
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 6 months ago by • 0
0
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6
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1.2k
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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631
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
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0
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282
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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
replies
623
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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744
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 months ago by ★ 4.5k • written 7 months ago by • 0
0
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1
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481
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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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436
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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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567
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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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841
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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553
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
479
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 7 months ago by ★ 4.5k • written 7 months ago by • 0
0
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2
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995
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 months ago kcarey • 0
2
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2
replies
511
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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545
views
DESeq2 Replicates
DESeq2 RNASeq
8 months ago kcarey • 0
1
vote
3
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657
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 9 months ago by ▴ 10
0
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4
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652
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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736
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 months ago by 52k • written 9 months ago by • 0
3
votes
5
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1.0k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 months ago by 43k • written 9 months ago by ▴ 10
2
votes
1
reply
484
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
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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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498
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
2
votes
2
replies
994
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
9 months ago jackafiore • 0
1
vote
2
replies
1.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 19 months ago by • 0
0
votes
4
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702
views
Ballgown error in scan for c.tab files
ballgown RNASeq
10 months ago candacenewcome • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: ANOVA like approach of edgeR by Gordon Smyth 52k
To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …
Comment: DESeq2 sizefactors counfounded with biological treatment by Anna • 0
Hi James, Apologies (re: posting in the wrong place). Thank you so much for your response, that was exactly the help I needed. Best, A…
Comment: ANOVA like approach of edgeR by Talip ▴ 10
I am comparing the expression patterns of different tissue cell lines (CellType) under five distinct media conditions (Status). Since the c…
Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 160
It is almost always better to retain the full observed data, if the statistical software is able to model the repeated measures. This is a…
Comment: makeContrastsDream for Interaction by gabriel.hoffman ▴ 160
The simplest way to handle contrasts with an interaction term is to create a new variable. Lets consider a simpler case with variables `Se…
Votes
Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
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