Showing : RNASEQ • reset
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 19 days ago by • 0
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0
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117
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
20 days ago GT • 0
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2
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366
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WGCNA
WGCNA Normalization RNASeq
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
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3
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581
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
1
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2
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1.1k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
0
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1
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169
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
0
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3
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441
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 weeks ago by • 0 • written 10 weeks ago by ▴ 10
0
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1
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244
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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2
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565
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
9 weeks ago • updated 7 weeks ago ingrid.h • 0
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4
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1.0k
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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
10 weeks ago • updated 9 weeks ago Quang NN ▴ 10
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3
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 weeks ago by • 0
4
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2
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572
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
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5
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698
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Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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2
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588
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
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1
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338
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
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5
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734
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 4 months ago by • 0
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1
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233
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eRNAs count
RNASeq DESeq2
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
1
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8
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1.7k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
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0
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219
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
5 months ago brayas13 • 0
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11
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1.0k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
2
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4
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587
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
5 months ago jihoon.kim.1495 ▴ 10
1
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1
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574
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 6 months ago by 68k • written 6 months ago by • 0
1
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2
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621
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 6 months ago by ▴ 10
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3
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692
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
6 months ago Travis • 0
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5
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1.9k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.9 years ago by • 0
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2
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1.2k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
3
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5
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1.7k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 7 months ago by ★ 1.4k • written 8 months ago by • 0
2
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3
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831
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
7 months ago BioinfGuru ▴ 70
3
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6
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994
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 8 months ago by • 0
4
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3
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1.4k
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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 8 months ago by ▴ 10
0
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3
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714
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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 8 months ago by ★ 4.8k • written 8 months ago by • 0
1
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4
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1.9k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
9 months ago • updated 8 months ago Lucy ▴ 60
0
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4
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761
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
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492
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
9 months ago JG13 • 0
0
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1
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481
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 9 months ago by 68k • written 9 months ago by • 0
1
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9
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2.3k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 9 months ago by 68k • written 9 months ago by ▴ 10
1
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3
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743
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 9 months ago by 68k • written 9 months ago by ▴ 50
2
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2
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778
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 10 months ago by • 0
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6
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1.7k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
10 months ago atan • 0
3
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2
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860
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
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403
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
10 months ago Bibi • 0
10
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11
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2.6k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 10 months ago by • 0 • written 7.6 years ago by ▴ 80
1
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3
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810
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
0
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3
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1.1k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
0
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1
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665
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
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564
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 months ago by • 0
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2
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827
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 months ago catv • 0
5
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3
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1.2k
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 months ago by 52k • written 11 months ago by • 0
0
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1
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928
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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1
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725
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
50 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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