Showing : RNAseq • reset
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 5 days ago by • 0
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0
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63
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 days ago GT • 0
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2
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346
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WGCNA
WGCNA Normalization RNASeq
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
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3
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551
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 29 days ago by 43k • written 4 weeks ago by • 0
1
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2
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1.0k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 5 weeks ago by ★ 4.7k • written 5 weeks ago by • 0
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1
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158
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
0
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3
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415
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 8 weeks ago by ▴ 10
0
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1
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230
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
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2
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550
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
7 weeks ago • updated 5 weeks ago ingrid.h • 0
0
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4
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973
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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
8 weeks ago • updated 7 weeks ago Quang NN ▴ 10
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3
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571
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 weeks ago by • 0
4
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2
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534
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
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5
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675
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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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571
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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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307
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
1
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5
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699
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 4 months ago by • 0
0
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1
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226
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eRNAs count
RNASeq DESeq2
updated 4 months ago by ★ 4.7k • 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 4 months ago by • 0
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0
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205
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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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1.0k
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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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561
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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
537
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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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607
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 6 months ago by ▴ 10
0
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3
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653
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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
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
3
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5
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1.5k
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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 7 months ago by • 0
2
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3
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796
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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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954
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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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1.3k
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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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688
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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 ★ 4.7k • written 8 months ago by • 0
1
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4
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1.8k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
8 months ago Lucy ▴ 60
0
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4
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740
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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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464
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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
reply
470
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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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2.2k
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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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715
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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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758
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 9 months ago by ▴ 10 • written 10 months ago by • 0
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 • updated 9 months ago atan • 0
3
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2
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835
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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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394
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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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789
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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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1.0k
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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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647
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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
0
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2
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554
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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
0
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2
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796
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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
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 11 months ago by • 0
0
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1
reply
875
views
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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700
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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