Showing : RNASeq • reset
5
votes
3
replies
267
views
Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 22 days ago by • 0
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
3
replies
173
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
0
votes
2
replies
175
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 18 days ago by • 0
0
votes
1
reply
160
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 days ago by 42k • written 16 days ago by • 0
1
vote
3
replies
874
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 16 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
votes
2
replies
223
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
21 days ago • updated 18 days ago catv • 0
0
votes
1
reply
118
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 22 days ago by 42k • written 22 days ago by • 0
0
votes
2
replies
930
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 23 days ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
145
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 5 weeks ago by 50k • written 11.5 years ago by ▴ 30
0
votes
2
replies
705
views
biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 7 weeks ago by • 0 • written 9.0 years ago by ▴ 150
0
votes
2
replies
245
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
7 weeks ago kcarey • 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 7 weeks ago by • 0 • written 7.6 years ago by • 0
0
votes
2
replies
291
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 weeks ago kcarey • 0
2
votes
2
replies
272
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
0
votes
2
replies
1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 8 weeks ago by • 0 • written 2.7 years ago by • 0
1
vote
4
replies
313
views
DESeq2 Replicates
DESeq2 RNASeq
9 weeks ago kcarey • 0
1
vote
3
replies
374
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by ▴ 10
0
votes
3
replies
503
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
3
votes
5
replies
644
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 11 weeks ago by ▴ 10
0
votes
4
replies
311
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago mperalc • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
0
votes
2
replies
320
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
1
reply
271
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
3
votes
6
replies
554
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 weeks ago boczniak767 ▴ 720
0
votes
0
replies
230
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
12 weeks ago Abril • 0
4
votes
6
replies
616
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
2
replies
423
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
414
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
344
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
602
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
241
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
610
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
3
votes
1
reply
312
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
0
votes
1
reply
273
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
2
replies
479
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
2
replies
1.4k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 15 months ago by • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
7
replies
857
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
2
replies
453
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
7
votes
2
replies
826
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, 20 minutes ago
Canada, 38 minutes ago
United States, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 356 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6