Showing : RNAseq • reset
17
votes
14
replies
53k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.3 years ago by • 0 • written 8.2 years ago by ▴ 20
0
votes
4
replies
3.6k
views
DESeq2 using interaction terms or grouping variable
deseq2 rnaseq
8.2 years ago rrcutler ▴ 70
1
vote
2
replies
2.7k
views
How to adjust for different cell type mixtures in differential expression analysis?
cell types differential expression adjustment mixtures rnaseq
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by ▴ 90
3
votes
2
replies
1.3k
views
Batch effect between paired and single ended reads
rnaseq
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 420
2
votes
5
replies
2.5k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
8.3 years ago Nicholas Owen • 0
5
votes
15
replies
6.7k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 2.3 years ago by 68k • written 8.3 years ago by ▴ 10
1
vote
7
replies
2.2k
views
Low number differentially expressed genes with DESeq2, want to estimate dispersion gene-wise
DESeq2 RNASeq differential gene expression
10.5 years ago • updated 8.3 years ago A • 0
2
votes
6
replies
2.8k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq limma voom anova
updated 3.6 years ago by ▴ 100 • written 8.3 years ago by ▴ 90
9
votes
7
replies
13k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 8.3 years ago by ▴ 10 • written 8.3 years ago by ▴ 30
0
votes
1
reply
1.2k
views
RNAseq Analysis using RUVs
rnaseq ruvseq r
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by • 0
0
votes
1
reply
1.4k
views
EdgeR dispersion and FDR
edger FDR rnaseq
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
0
votes
1
reply
1.9k
views
How to generate heatmap for three groups
rnaseq ruvseq heatmap
updated 8.3 years ago by 68k • written 8.3 years ago by • 0
0
votes
0
replies
1.2k
views
Differential expressed genes between different samples in RUVseq
rnaseq ruv differential gene expression R
8.3 years ago manish20072013 • 0
2
votes
1
reply
1.6k
views
Decide normalisation method in RUVseq for RNAseq data
edger ruvseq rnaseq normalization ruvnormalize
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by • 0
6
votes
4
replies
7.2k
views
RNAseq with technical replicates: Does it sound right?
rnaseq edger technical replicates
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by ▴ 130
1
vote
8
replies
7.8k
views
How to perform DESeq2 based on paired sample test?
rnaseq deseq2
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 20
0
votes
1
reply
2.6k
views
how to use q value to select differentially expressed genes
rnaseq
updated 8.3 years ago by ▴ 760 • written 8.3 years ago by • 0
4
votes
5
replies
1.9k
views
Warning: missing reverse strand option in easyRNASeq.
easyrnaseq rnaseq strand
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 10
3
votes
1
reply
5.9k
views
Creating a count matrix from 8 bam files in R (RNAseq experiment)
deseq2 rnaseq count matrix galignments granges
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 10
2
votes
3
replies
3.2k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
3
votes
4
replies
1.4k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
0
votes
4
replies
2.1k
views
setting contrast in edgeR for time series data
rnaseq edger makecontrasts
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
0
votes
3
replies
2.4k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
1
vote
1
reply
2.0k
views
Manually adding IRanges/GRanges to DESeq dataset?
deseq2 rnaseq
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
votes
1
reply
2.4k
views
exon counting with featureCounts
RNAseq
8.4 years ago inah ▴ 10
0
votes
5
replies
3.7k
views
Which raw files (RNAseq) to download?
bioconductor rnaseq
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
4
votes
1
reply
2.4k
views
WGCNA always requires trait data?
wgcna rnaseq
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Are significant genes ordered in maSigPro?
masigpro rnaseq
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
votes
3
replies
1.5k
views
Dr. Armin Ahmadvand
R rnaseq
8.4 years ago ahmadvandra • 0
0
votes
0
replies
1.5k
views
CummeRbund volcano plot infinite values
cummerbund rnaseq
8.4 years ago niu.shengyong ▴ 10
0
votes
0
replies
1.1k
views
Regarding featureCounts and Rsubread
rnaseq
8.4 years ago sancharisircar24 • 0
1
vote
5
replies
3.4k
views
DESeq2: How to find out how well the model fits the data?
rnaseq linear model fit deseq2
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
1
vote
0
replies
2.2k
views
Problem about module preservation statistics in WGCNA software
rnaseq tcga wgcna
8.5 years ago • updated 8.4 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
1.3k
views
installing getgo package
rnaseq goseq package installation
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
5
votes
4
replies
1.7k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 8.4 years ago by • 0 • written 8.4 years ago by ▴ 40
0
votes
4
replies
4.0k
views
DESeq2 extracting results: resultsNames does not show the expected output
deseq2 rnaseq resultsnames
8.5 years ago • updated 8.4 years ago zeynep.nenseth • 0
1
vote
6
replies
1.6k
views
Clarification requested for the RNAseq Gene workflow document
deseq2 rnaseq
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Change DEXSeq plot: Intron length/width and genes from - strand
rnaseq r dexseq visualization
8.4 years ago aleipz • 0
1
vote
2
replies
1.4k
views
Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
0
votes
3
replies
1.5k
views
DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
rnaseq deseq2 ensembl
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
1
vote
2
replies
1.7k
views
rowRanges in Summarized Experiment changes counts
deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
2
votes
4
replies
2.0k
views
Search for Drugs related to results of differential expression analysis using RNA-seq
rnaseq drugvsdisease gcmap gcmapweb
updated 8.4 years ago by • 0 • written 8.5 years ago by ▴ 20
0
votes
6
replies
3.4k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
0
votes
4
replies
23k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2 rnaseq R
8.5 years ago zeynep.nenseth • 0
0
votes
7
replies
3.2k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2 confounders design matrix rnaseq
8.5 years ago lina.faller ▴ 10
0
votes
1
reply
1.3k
views
DESeq2 "unmix" function
deseq2 rnaseq
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
1
vote
7
replies
2.3k
views
DESeq2: use of unmix() function for deconvolution of whole blood
deseq2 bioconductor rnaseq differential gene expression
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
0
votes
1
reply
955
views
Scater: mito.drop on an absolute value ?
rnaseq scater
8.5 years ago maria.vladoiu • 0
0
votes
3
replies
2.7k
views
RNAseq read coverage plot: What tool?
rnaseq visualization plotcoveragehist
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 130
0
votes
3
replies
1.2k
views
DESeq2 for single gene
deseq2 rnaseq
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
1,409 results • Page 17 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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