Showing : RNAseq • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 24 days ago by 53k • written 28 days ago by • 0
0
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0
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113
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 20 days ago by 43k • written 6 weeks ago by • 0
5
votes
13
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1.1k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 weeks ago by 53k • written 7 weeks ago by • 0
0
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1
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3.1k
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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 11.0 years ago by • 0
2
votes
9
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885
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
11 weeks ago mohammedtoufiq91 ▴ 10
0
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8
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578
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
12 weeks ago • updated 11 weeks ago Jiahao Tian • 0
3
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11
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2.0k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 months ago by • 0
3
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2
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841
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
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5
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774
views
WGCNA
WGCNA Normalization RNASeq
written 8 months ago by • 0
3
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2
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1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
0
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1
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522
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 5 months ago by • 0
2
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5
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1.3k
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Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 5 months ago by ▴ 110 • written 5 months ago by ▴ 10
0
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0
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277
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
5 months ago dudwnsrla1 • 0
4
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7
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3.2k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 23 days 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 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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4
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1.1k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 7 months ago by • 0
0
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0
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439
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
7 months ago GT • 0
0
votes
3
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933
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
1
vote
2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
1
reply
378
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 months ago by 43k • written 8 months ago by • 0
0
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3
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828
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 9 months ago by ▴ 10
0
votes
1
reply
532
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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852
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
9 months ago • updated 8 months ago ingrid.h • 0
0
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4
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1.3k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 months ago Quang NN ▴ 10
0
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3
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872
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 9 months ago by • 0
4
votes
2
replies
958
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 10
1
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5
replies
997
views
Deseq2 Design
RNASeq DESeq2
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
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864
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 months ago by 53k • written 10 months ago by ▴ 10
0
votes
1
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635
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
vote
5
replies
1.1k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 11 months ago by • 0
0
votes
1
reply
400
views
eRNAs count
RNASeq DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
vote
8
replies
2.4k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 months ago by • 0
0
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0
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379
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
12 months ago brayas13 • 0
2
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4
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848
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
976
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 13 months ago by 68k • written 13 months ago by • 0
1
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2
replies
854
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
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3
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1.1k
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
13 months ago Travis • 0
0
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5
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2.2k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.5 years ago by • 0
0
votes
2
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1.5k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 14 months ago by ★ 1.4k • written 15 months ago by • 0
2
votes
3
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1.2k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
14 months ago BioinfGuru ▴ 70
3
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6
replies
1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 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 15 months ago by ▴ 10
0
votes
3
replies
961
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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4
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2.5k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
15 months ago Lucy ▴ 60
0
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4
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1.0k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 15 months ago by • 0
0
votes
0
replies
682
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
16 months ago JG13 • 0
0
votes
1
reply
671
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 16 months ago by 68k • written 16 months ago by • 0
1
vote
9
replies
3.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 16 months ago by 68k • written 16 months ago by ▴ 10
1
vote
3
replies
981
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
1,409 results • Page 1 of 29
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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