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0
votes
0
replies
810
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
3.4 years ago
Tamina
• 0
0
votes
1
reply
1.5k
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq
Correlation
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
keshav.prasad.gubbi
• 0
1
vote
3
replies
2.0k
views
Strange Dispersion plot
DESeq2
3.4 years ago
Yiqi
▴ 10
0
votes
1
reply
1.1k
views
Correlation between CpG methylation and gene expression from DESeq2-> Normalization of counts using VST + fpkm/rpkm for optimal normalization?
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
Brendon Herring
• 0
1
vote
0
replies
885
views
How can I properly decode error when using ASICS?
ASICSdata
ASICS
3.4 years ago
nep63
▴ 10
2
votes
2
replies
2.1k
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
3.4 years ago
Fatemeh
• 0
0
votes
0
replies
914
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
3.4 years ago
Jonathan
• 0
1
vote
1
reply
1.3k
views
GSEA with Wikipathways not entirely reproducible
clusterProfiler
updated 3.4 years ago by
Guido Hooiveld
★ 4.1k • written 3.4 years ago by
Susana
• 0
2
votes
8
replies
3.2k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
written 3.4 years ago by
bpshtiwan
▴ 10
0
votes
2
replies
1.9k
views
Retrieve gene summary start/end in biomart query
biomaRt
3.4 years ago
rbenel
▴ 50
1
vote
4
replies
9.9k
views
TPM normalization starting with read counts
edgeR
DESeq2
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
JAcky
• 0
4
votes
1
reply
2.3k
views
Adding custom transcript to Salmon index
salmon
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
Ray
▴ 20
0
votes
2
replies
2.9k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 3.4 years ago by
Tiago C. Silva
▴ 270 • written 3.6 years ago by
JAcky
• 0
2
votes
7
replies
3.2k
views
error running UniProt.ws
UniProt.ws
updated 3.4 years ago by
Marcel Ramos
700 • written 3.5 years ago by
julien.wollbrett
▴ 10
0
votes
8
replies
1.8k
views
errors in annotation
org.Bt.eg.db
3.4 years ago
Josie
• 0
0
votes
1
reply
934
views
DESeq errpr in normalizePath
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
ummscr
• 0
2
votes
2
replies
1.2k
views
paired samples, comparing expression given a continuous variable
limma
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
naz
• 0
0
votes
0
replies
864
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
3.4 years ago
osieman52
• 0
0
votes
0
replies
1.0k
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
3.4 years ago
Hector
• 0
3
votes
2
replies
1.7k
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
3.4 years ago
Jiping Wang
▴ 90
0
votes
0
replies
1.1k
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
3.4 years ago
calen.p.ryan
• 0
1
vote
2
replies
1.4k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.4 years ago
Delta._.43
▴ 20
1
vote
1
reply
1.3k
views
spot- vs cell-level data access
spatialLIBD
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.4 years ago by
kstern
• 0
2
votes
3
replies
2.2k
views
unable to install.packages("spatialLIBD")
spatialLIBD
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.4 years ago by
kstern
• 0
1
vote
0
replies
909
views
Normalization RNA-seq data maSigPro
maSigPro
3.4 years ago
W.a.m.dekker
▴ 10
0
votes
2
replies
1.4k
views
MAI error - vector size limit
randomForest
MAI
updated 3.4 years ago by
jonathan.dekermanjian
• 0 • written 3.5 years ago by
Hans-Ulrich Klein
▴ 330
1
vote
0
replies
1.2k
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
3.4 years ago
arisarkar88
▴ 40
0
votes
2
replies
1.6k
views
OPLS-DA: confidence interval for accuracy metric
Metabolomics
3.4 years ago
Eddie
• 0
0
votes
2
replies
2.4k
views
Error in trying to use Interactive analysis using the DEP Shiny apps (LFQ app)
LFQ
updated 3.4 years ago by
Malcolm Cook
★ 1.6k • written 3.9 years ago by
maria.kokolaki
• 0
1
vote
1
reply
924
views
ordinal treatment group design / contrast matrix
limma
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Chris
• 0
0
votes
1
reply
1.6k
views
Change my bedgraph file to wig in R
bedgraph
R
wig
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
margo
• 0
0
votes
2
replies
975
views
Question regarding averaging DESeq2 results.
DESeq2
3.4 years ago
e.v.egeland
• 0
0
votes
2
replies
1.4k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
3.4 years ago
Marie
• 0
0
votes
1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.4 years ago by
shepherl
4.3k • written 3.4 years ago by
dheeraj.raya
• 0
0
votes
5
replies
3.6k
views
Issues installing DESeq2 package with R version 4.2.1
DESeq2
3.4 years ago
lucabartolinimd
• 0
0
votes
0
replies
821
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
3.4 years ago
04.marshal-decibel
• 0
0
votes
3
replies
2.8k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 3.4 years ago by
Marcel Ramos
700 • written 3.4 years ago by
kikiki
• 0
0
votes
1
reply
2.0k
views
error in function useDataset of biomaRt
bioma
biomaRt
updated 3.4 years ago by
Basti
▴ 780 • written 3.4 years ago by
Riley Qiu
• 0
4
votes
5
replies
4.6k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
3.5 years ago • updated 3.4 years ago
Peter Hickey
▴ 760
4
votes
2
replies
2.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
3.4 years ago
Guandong Shang
▴ 40
0
votes
4
replies
3.1k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 3.4 years ago by
Aaron Lun
★ 29k • written 3.5 years ago by
Guandong Shang
▴ 40
2
votes
2
replies
2.4k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
Muhammad
• 0
4
votes
5
replies
3.6k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
Yang Shi
▴ 10
1
vote
1
reply
1.1k
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
3.4 years ago
mehdi
• 0
0
votes
3
replies
1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
3.4 years ago
abf
▴ 30
4
votes
13
replies
5.8k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 3.6 years ago by
etiennedanis
• 0
1
vote
1
reply
855
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq
DESeq2
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
seeta_rajpara
• 0
2
votes
5
replies
1.7k
views
Detection of reference genes by Deseq2
lessAbs
reference_genes
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
sj
▴ 10
4
votes
3
replies
2.8k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 3.4 years ago by
James W. MacDonald
68k • written 3.5 years ago by
achoppe
▴ 10
1
vote
5
replies
2.0k
views
batch effect
TargetScoreData
batchelor
written 3.5 years ago by
Syed Zaheer
▴ 10
46,723 results • Page
80 of 935
Recent ...
Replies
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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