Showing : edger • reset
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
7
votes
2
replies
698
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
6
votes
7
replies
894
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 5 months ago by ★ 4.0k • written 6 months ago by ▴ 20
6
votes
8
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 3 days ago by • 0 • written 14 months ago by ▴ 10
6
votes
7
replies
528
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
6
votes
2
replies
690
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
9 months ago Josué ▴ 20
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 10 months ago by ▴ 20
5
votes
2
replies
496
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
5
votes
9
replies
2.4k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 7 months ago by • 0 • written 6.4 years ago by ▴ 10
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
5
votes
4
replies
357
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
8 weeks ago • updated 7 weeks ago pl23 • 0
5
votes
6
replies
343
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 3 days ago by ★ 4.0k • written 7 days ago by ▴ 30
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 10 months ago by 50k • written 10 months ago by ▴ 10
5
votes
3
replies
658
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 19 days ago by 50k • written 26 days ago by ▴ 50
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 21 months ago by ▴ 30
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
8 months ago Luca • 0
4
votes
4
replies
410
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 11 weeks ago by 65k • written 3 months ago by • 0
4
votes
2
replies
567
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
4
votes
3
replies
1.7k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.0k
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 8 months ago by 50k • written 8 months ago by • 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 6 months ago by • 0 • written 3.1 years ago by • 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
3
votes
4
replies
688
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
3
votes
3
replies
531
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 12 months ago by 50k • written 10.0 years ago by ★ 1.0k
3
votes
5
replies
319
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 16 days ago by 50k • written 18 days ago by • 0
3
votes
2
replies
652
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 9 months ago by 50k • written 9 months ago by ▴ 10
3
votes
2
replies
355
views
How does one test for interactions in EdgeR?
edgeR
9 weeks ago pl23 • 0
3
votes
6
replies
809
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
1
reply
1.6k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
3
votes
3
replies
619
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 10 weeks ago by • 0 • written 10.8 years ago by ▴ 30
3
votes
4
replies
354
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
3
votes
3
replies
555
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 6 months ago by 65k • written 7 months ago by • 0
3
votes
3
replies
226
views
permutation test in edgeR
rna-seq edgeR
updated 1 day ago by 50k • written 8 days ago by • 0
2
votes
1
reply
626
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 11 months ago by 50k • written 11 months ago by • 0
2
votes
2
replies
231
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 weeks ago Sabiha ▴ 20
2
votes
3
replies
259
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 28 days ago by 50k • written 29 days ago by • 0
2
votes
2
replies
231
views
between lane normalization upper quantile
EDASeq edgeR
4 weeks ago • updated 29 days ago elesofi • 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 7 months ago by • 0 • written 6.3 years ago by • 0
2
votes
6
replies
371
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
8 weeks ago tsl0026 • 0
2
votes
3
replies
325
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
8
replies
2.2k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 10 months ago Luis • 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
2
votes
1
reply
594
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
2
votes
4
replies
514
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 weeks ago Sabiha ▴ 20
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 20
2
votes
3
replies
779
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
8 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
618
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Answer: List of Deprecated Packages for Bioc3.18 by shepherl 3.8k
previously unannounced, COHCAP is not deprecated but removed with release 3.19. see [mailing list discussion](https://stat.ethz.ch/piperm…
Answer: SNP locus package for mouse? by James W. MacDonald 65k
There isn't (IIRC) an official way to do this, but [Herve has a GitHub][1] with a package that you could use if you are willing to put in t…
Votes
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
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