Showing : RNAseq • reset
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WGCNA
WGCNA Normalization RNASeq
updated 18 days ago by • 0 • written 19 days ago by • 0
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3
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524
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 17 days ago by 43k • written 20 days ago by • 0
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2
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1.0k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 24 days ago by ★ 4.7k • written 24 days ago by • 0
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1
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146
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 27 days ago by 43k • written 4 weeks ago by • 0
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3
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389
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 6 weeks ago by ▴ 10
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1
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203
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
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2
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535
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
5 weeks ago • updated 24 days ago ingrid.h • 0
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4
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964
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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 weeks ago • updated 5 weeks ago Quang NN ▴ 10
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3
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551
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 weeks ago by • 0
4
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2
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491
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 11 weeks ago by ★ 4.7k • written 12 weeks ago by ▴ 10
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5
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641
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Deseq2 Design
RNASeq DESeq2
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
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2
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549
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
0
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1
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287
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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5
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653
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 3 months ago by • 0
0
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1
reply
214
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eRNAs count
RNASeq DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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8
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1.6k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
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0
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196
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
4 months ago brayas13 • 0
3
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11
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948
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 months ago by • 0
2
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4
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535
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
5 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
504
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 months ago by 68k • written 5 months ago by • 0
1
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2
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586
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
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3
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622
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 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 3.8 years ago by • 0
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2
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1.1k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
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5
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1.4k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
2
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3
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756
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
7 months ago • updated 6 months ago BioinfGuru ▴ 70
3
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6
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927
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 7 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 7 months ago by ▴ 10
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3
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673
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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 7 months ago by ★ 4.7k • written 7 months ago by • 0
1
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4
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1.7k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
8 months ago • updated 7 months ago Lucy ▴ 60
0
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4
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724
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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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0
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449
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
8 months ago JG13 • 0
0
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1
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458
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 8 months ago by 68k • written 8 months ago by • 0
1
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9
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2.1k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 8 months ago by 68k • written 9 months ago by ▴ 10
1
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3
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705
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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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741
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
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6
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1.6k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
9 months ago atan • 0
3
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2
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815
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
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0
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386
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
9 months ago Bibi • 0
10
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11
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2.6k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 9 months ago by • 0 • written 7.6 years ago by ▴ 80
1
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3
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767
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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
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3
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1.0k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 10 months ago by ★ 4.7k • written 10 months ago by • 0
0
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1
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635
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
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2
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536
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 months ago by • 0
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2
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766
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
5
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3
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1.1k
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
0
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1
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831
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
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684
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 11 months ago by ★ 4.7k • written 11 months ago by • 0
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2
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1.5k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
11 months ago kcarey • 0
2
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2
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611
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
12 months ago Sabiha ▴ 20
50 results • Page 1 of 1
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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