Showing : RNAseq • reset
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Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
4 days ago lianov • 0
3
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6
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981
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 7 weeks ago by • 0
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2
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493
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 5 weeks ago by • 0 • written 3 months ago by • 0
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1
reply
243
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
5
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13
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1.4k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 3 months ago by 53k • written 4 months ago by • 0
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1
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3.2k
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Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.2 years ago by • 0
2
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9
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1.0k
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
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8
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683
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
3
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13
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2.2k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
3
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2
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963
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
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5
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952
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WGCNA
WGCNA Normalization RNASeq
written 10 months ago by • 0
3
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2
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1.5k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
0
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1
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623
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
2
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5
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1.5k
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Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 7 months ago by ▴ 110 • written 7 months ago by ▴ 10
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0
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346
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
7 months ago dudwnsrla1 • 0
4
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7
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3.4k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
8 months ago • updated 3 months ago massimo ▴ 10
1
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1
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1.3k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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4
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1.4k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 9 months ago by • 0
0
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0
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533
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
9 months ago GT • 0
0
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3
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1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
1
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2
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1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 10 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
reply
454
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
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977
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 months ago by • 0 • written 11 months ago by ▴ 10
0
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1
reply
698
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
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2
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999
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
11 months ago ingrid.h • 0
0
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4
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1.4k
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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
11 months ago Quang NN ▴ 10
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3
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1.0k
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 months ago by • 0
4
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2
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1.1k
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 12 months ago by ★ 5.0k • written 13 months ago by ▴ 10
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5
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1.1k
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Deseq2 Design
RNASeq DESeq2
updated 12 months ago by 68k • written 13 months ago by • 0
0
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2
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977
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 13 months ago by 53k • written 13 months ago by ▴ 10
0
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1
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770
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
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5
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1.3k
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 13 months ago by • 0
0
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1
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460
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eRNAs count
RNASeq DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
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8
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2.6k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
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0
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416
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
14 months ago brayas13 • 0
2
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4
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981
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
1
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1
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1.1k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
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2
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942
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
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3
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1.3k
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
15 months ago Travis • 0
0
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5
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2.3k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
0
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2
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1.7k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
3
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5
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2.5k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
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3
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1.4k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
17 months ago BioinfGuru ▴ 70
3
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6
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1.4k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 17 months ago by • 0
4
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3
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1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 18 months ago by ▴ 10
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3
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1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
1
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4
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2.8k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
18 months ago • updated 17 months ago Lucy ▴ 60
0
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4
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1.1k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 18 months ago by • 0
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0
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754
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
18 months ago JG13 • 0
0
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1
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768
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1,411 results • Page 1 of 29
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
Answer: Where do the filename come from in the LOLA datasets?
Bioconductor Maintainer Application
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
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