Showing : RNAseq • reset
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 2 days ago by 43k • written 3 days ago by • 0
0
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1
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172
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
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4
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871
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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
6 days ago • updated 3 days ago Quang NN ▴ 10
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2
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211
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
6 days ago • updated 4 days ago Quang NN ▴ 10
0
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2
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376
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
23 days ago • updated 21 days ago sindhuri • 0
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2
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329
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
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5
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573
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Deseq2 Design
RNASeq DESeq2
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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2
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497
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 8 weeks ago by 52k • written 8 weeks ago by ▴ 10
0
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1
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217
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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5
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543
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 10 weeks ago by • 0
0
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1
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178
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eRNAs count
RNASeq DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 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 12 weeks ago by • 0
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0
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176
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
12 weeks ago brayas13 • 0
3
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11
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863
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
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4
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484
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
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1
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424
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 4 months ago by 67k • written 4 months ago by • 0
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2
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530
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
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3
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482
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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
views
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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987
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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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1.2k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
2
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3
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637
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
3
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6
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881
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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
views
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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627
views
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
6 months ago Lucy ▴ 60
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4
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657
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
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0
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400
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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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418
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 7 months ago by 67k • written 7 months ago by • 0
1
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9
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1.8k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
1
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3
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640
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
2
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2
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689
views
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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1.4k
views
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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737
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
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344
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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 7.4 years ago by ▴ 80
1
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3
replies
717
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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3
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899
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
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1
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577
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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503
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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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668
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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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1.0k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 9 months ago by • 0
0
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1
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694
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
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603
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
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2
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1.2k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
10 months ago kcarey • 0
2
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2
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572
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
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2
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1.7k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago kcarey • 0
1
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4
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609
views
DESeq2 Replicates
DESeq2 RNASeq
11 months ago kcarey • 0
1
vote
3
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759
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
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4
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721
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 months ago mperalc • 0
50 results • Page 1 of 1
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Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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