Showing : RnaSeq • reset
1
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 1 day ago by ★ 4.7k • written 2 days ago by • 0
0
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1
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112
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 5 days ago by 43k • written 9 days ago by • 0
0
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3
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329
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 13 days ago by • 0 • written 21 days ago by ▴ 10
0
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1
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133
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 17 days ago by 43k • written 18 days ago by • 0
0
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2
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485
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
19 days ago • updated 2 days ago ingrid.h • 0
0
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4
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916
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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
21 days ago • updated 18 days ago Quang NN ▴ 10
0
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3
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509
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 5 weeks ago by • 0
4
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2
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430
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 8 weeks ago by ★ 4.7k • written 9 weeks ago by ▴ 10
1
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5
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605
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Deseq2 Design
RNASeq DESeq2
updated 8 weeks ago by 68k • written 9 weeks ago by • 0
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2
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510
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 10
0
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1
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240
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 weeks ago by ★ 4.7k • written 12 weeks ago by • 0
0
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5
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578
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 12 weeks ago by • 0
0
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1
reply
194
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eRNAs count
RNASeq DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
1
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8
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1.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
0
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0
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181
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
3 months ago brayas13 • 0
3
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11
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888
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 months ago by • 0
2
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4
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502
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
4 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
455
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 4 months ago by 68k • written 4 months ago by • 0
1
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2
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555
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
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3
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533
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
4 months ago Travis • 0
0
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5
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1.8k
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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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1.0k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
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5
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1.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
2
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3
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679
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 months ago BioinfGuru ▴ 70
3
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6
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897
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 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
0
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3
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649
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 6 months ago by ★ 4.7k • written 6 months ago by • 0
1
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4
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1.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
7 months ago • updated 6 months ago Lucy ▴ 60
0
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4
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674
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 months ago by • 0
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0
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417
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
7 months ago JG13 • 0
0
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1
reply
430
views
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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1.9k
views
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 8 months ago by ▴ 10
1
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3
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656
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 8 months ago by 68k • written 8 months ago by ▴ 50
2
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2
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713
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 8 months ago by ▴ 10 • written 9 months ago by • 0
0
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6
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1.5k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
8 months ago atan • 0
3
votes
2
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767
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
0
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0
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360
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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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2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 9 months ago by • 0 • written 7.5 years ago by ▴ 80
1
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3
replies
736
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
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3
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939
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 9 months ago by ★ 4.7k • written 9 months ago by • 0
0
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1
reply
594
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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515
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 9 months ago by • 0
0
votes
2
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713
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
5
votes
3
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1.1k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 months ago by 52k • written 10 months ago by • 0
0
votes
1
reply
737
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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627
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 10 months ago by ★ 4.7k • written 10 months ago by • 0
0
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2
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1.3k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
11 months ago kcarey • 0
2
votes
2
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587
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
11 months ago Sabiha ▴ 20
0
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2
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1.8k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
11 months ago kcarey • 0
1
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4
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631
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DESeq2 Replicates
DESeq2 RNASeq
11 months ago kcarey • 0
50 results • Page 1 of 1
Recent ...
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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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