Showing : RNASEQ • reset
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 8 days ago by ★ 1.4k • written 8 days ago by • 0
3
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5
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633
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 25 days ago by ★ 1.4k • written 4 weeks ago by • 0
2
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3
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304
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
28 days ago • updated 25 days ago BioinfGuru ▴ 70
3
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6
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657
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 weeks ago by • 0
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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 7 weeks ago by ▴ 10
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3
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445
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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 6 weeks ago by ★ 4.4k • written 6 weeks ago by • 0
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4
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1.1k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
8 weeks ago • updated 6 weeks ago Lucy ▴ 60
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4
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407
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 weeks ago by • 0
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215
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
10 weeks ago JG13 • 0
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1
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273
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 11 weeks ago by 67k • written 11 weeks ago by • 0
1
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9
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865
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 11 weeks ago by 67k • written 12 weeks ago by ▴ 10
1
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3
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423
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 12 weeks ago by 67k • written 12 weeks ago by ▴ 50
2
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2
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525
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 3 months ago by ▴ 10 • written 3 months ago by • 0
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6
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959
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
3 months ago atan • 0
3
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2
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437
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
3 months ago mohammedtoufiq91 ▴ 10
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206
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
3 months ago Bibi • 0
10
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11
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2.2k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 months ago by • 0 • written 7.0 years ago by ▴ 80
1
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3
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501
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 3 months ago by 51k • written 3 months ago by • 0
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3
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533
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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
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1
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343
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 months ago by 42k • written 4 months ago by • 0
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2
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362
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 4 months ago by • 0
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2
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440
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 months ago catv • 0
5
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3
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603
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 months ago by 51k • written 4 months ago by • 0
0
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1
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373
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 months ago by 42k • written 4 months ago by • 0
0
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1
reply
322
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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
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2
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674
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 months ago kcarey • 0
2
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2
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434
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 months ago Sabiha ▴ 20
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2
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707
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 months ago kcarey • 0
1
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4
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465
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DESeq2 Replicates
DESeq2 RNASeq
6 months ago kcarey • 0
1
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3
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559
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 10
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4
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555
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
6 months ago mperalc • 0
0
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2
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616
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 6 months ago by 51k • written 6 months ago by • 0
3
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5
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910
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 months ago by 42k • written 6 months ago by ▴ 10
2
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1
reply
416
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 6 months ago by 42k • written 6 months ago by ▴ 10
3
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6
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941
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Average biological replicates in RNA-seq
Mfuzz RNASeq
6 months ago boczniak767 ▴ 740
0
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0
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425
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
6 months ago Abril • 0
2
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2
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772
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
7 months ago jackafiore • 0
1
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2
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1.5k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 16 months ago by • 0
0
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4
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603
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Ballgown error in scan for c.tab files
ballgown RNASeq
7 months ago candacenewcome • 0
1
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3
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554
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
7 months ago island • 0
1
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3
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851
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 7 months ago by • 0
0
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1
reply
403
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 7 months ago by ▴ 210 • written 7 months ago by • 0
2
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4
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1.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
7 months ago Sabiha ▴ 20
4
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6
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900
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 7 months ago by 51k • written 7 months ago by • 0
3
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1
reply
503
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 7 months ago by 51k • written 7 months ago by • 0
0
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3
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866
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 8 months ago by • 0
0
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1
reply
442
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
8 months ago WS • 0
2
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3
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1.9k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 8 months ago by ★ 1.4k • written 9 months ago by • 0
1
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2
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693
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
8 months ago Sabiha ▴ 20
1
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2
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656
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
9 months ago drewhaydensteele • 0
50 results • Page 1 of 1
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Comment: SingleR Label.Ont by Stepah • 0
[Aussie Play][1] cares about its Australian players by offering a safe and secure gaming experience where there is never a dull moment. The…
Comment: ensemblVEP deprecation and how to reproduce by Vincent J. Carey, Jr. 6.7k
What aspect of ensemblVEP are you looking for? The vignette https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/in…
Answer: Help with design matrix for RNA-seq data using edgeR by Gordon Smyth 51k
This forum is intended to help with software usage and syntax rather than to answer research questions, and your question is a definitely a…
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
DESeq2 has a way of fixing the reference pseudo-sample used for normalization. In estimateSizeFactors man page, you will see an argument g…
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
Sorry - I requested this to be posted here, I will answer.
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Answer: Help with design matrix for RNA-seq data using edgeR
Answer: Should tSNE from biol. replicates look alike?
Answer: Should tSNE from biol. replicates look alike?
Comment: fgsea stuck in an infinite loop in the middle of the run
Answer: Empty Results from champ.DMP Despite Expected Output
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