Showing : Rnaseq • reset
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
3 days ago Sahil • 0
0
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3
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320
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 days ago by • 0 • written 15 days ago by ▴ 10
0
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1
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126
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 days ago by 43k • written 13 days ago by • 0
0
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1
reply
198
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
updated 12 days ago by ★ 4.1k • written 13 days ago by • 0
0
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4
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906
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
15 days ago • updated 13 days ago Quang NN ▴ 10
0
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3
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499
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
updated 6 days ago by • 0 • written 4 weeks ago by • 0
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2
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340
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 7 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
1
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5
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596
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Deseq2 Design
RNASeq DESeq2
updated 7 weeks ago by 68k • written 8 weeks ago by • 0
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2
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506
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 9 weeks ago by 52k • written 9 weeks ago by ▴ 10
0
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1
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228
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
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5
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565
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 12 weeks ago by • 0
0
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1
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188
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eRNAs count
RNASeq DESeq2
updated 12 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
1
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8
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1.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
0
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0
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178
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
3 months ago brayas13 • 0
3
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11
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878
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 months ago by • 0
2
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4
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494
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
4 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
443
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 4 months ago by 68k • written 4 months ago by • 0
1
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2
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548
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
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3
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515
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
4 months ago Travis • 0
0
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5
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1.8k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.7 years ago by • 0
0
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2
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1.0k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
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5
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1.3k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
2
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3
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662
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 months ago BioinfGuru ▴ 70
3
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6
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888
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 months ago by • 0
4
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3
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1.3k
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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 6 months ago by ▴ 10
0
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3
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644
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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 months ago by ★ 4.6k • written 6 months ago by • 0
1
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4
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1.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
7 months ago • updated 6 months ago Lucy ▴ 60
0
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4
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665
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 months ago by • 0
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0
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408
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
7 months ago JG13 • 0
0
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1
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423
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 7 months ago by 68k • written 7 months ago by • 0
1
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9
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1.8k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 68k • written 8 months ago by ▴ 10
1
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3
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649
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 8 months ago by 68k • written 8 months ago by ▴ 50
2
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2
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704
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 8 months ago by ▴ 10 • written 8 months ago by • 0
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6
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1.5k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
8 months ago atan • 0
3
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2
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749
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
0
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0
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354
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
10
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11
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2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 8 months ago by • 0 • written 7.5 years ago by ▴ 80
1
vote
3
replies
725
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
3
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922
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
0
votes
1
reply
589
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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510
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 9 months ago by • 0
0
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2
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689
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago catv • 0
5
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3
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1.1k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
1
reply
714
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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1
reply
612
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
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2
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1.3k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
10 months ago kcarey • 0
2
votes
2
replies
582
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
11 months ago Sabiha ▴ 20
0
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2
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1.7k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
11 months ago kcarey • 0
1
vote
4
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624
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DESeq2 Replicates
DESeq2 RNASeq
11 months ago kcarey • 0
1
vote
3
replies
769
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp by Ian D. ▴ 70
Please can you comment on this @rory.
Comment: Why the order of sample names in the beta matrix affect the analysis results of by 81becky • 0
It sounds like you're experiencing a common issue with data alignment in Champ.DMP. Ensure that your beta matrix and PD files are consisten…
Comment: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by Blair • 0
@[Sprunki][1] wrote: Please read the vignette and think about adhering to the author's best practice, which discusses batch impacts. [1…
Comment: error in ChAMP loading file by 81becky • 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Votes
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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