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0
votes
4
replies
114
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
2 days ago • updated 1 minute ago
lonn
• 0
0
votes
1
reply
41
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 5 hours ago by
deeenes
▴ 30 • written 9 hours ago by
fernanda.backsouza
• 0
0
votes
1
reply
41
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
updated 6 hours ago by
Gordon Smyth
50k • written 15 hours ago by
catv
• 0
1
vote
1
reply
828
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 7 hours ago by
russ.bainer
▴ 10 • written 13 months ago by
jose.ramirez1
▴ 10
14
votes
20
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 8 hours ago
Chris
• 0
1
vote
2
replies
192
views
How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 11 hours ago
Weiqian
▴ 10
1
vote
0
replies
88
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
17 hours ago • updated 12 hours ago
BioinfGuru
▴ 30
0
votes
0
replies
22
views
FDR via q-value
qvalue
12 hours ago
John
• 0
0
votes
6
replies
557
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 13 hours ago
shepherl
3.8k
0
votes
4
replies
189
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 14 hours ago
Jonathan
▴ 10
0
votes
7
replies
352
views
DESeq filtering specific to contrasts
DESeq2
updated 14 hours ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
5
votes
14
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 15 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
2
replies
218
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 15 hours ago
isaac.vock
• 0
0
votes
3
replies
53
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 15 hours ago by
James W. MacDonald
65k • written 16 hours ago by
bas_work
▴ 30
2
votes
5
replies
666
views
DESeq2 setting significant p-value
DESeq2
updated 16 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
72
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 17 hours ago by
James W. MacDonald
65k • written 1 day ago by
sansan
• 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 17 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
199
views
DEG with low counts
DESeq2
updated 18 hours ago by
Michael Love
41k • written 5 days ago by
Rajat
• 0
6
votes
5
replies
380
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
0
votes
3
replies
76
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 20 hours ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
0
votes
2
replies
55
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
22 hours ago • updated 20 hours ago
prity6459
• 0
0
votes
1
reply
67
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 21 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
0
votes
2
replies
889
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
304
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 1 day ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 1 day ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
81
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago
sropri
• 0
1
vote
2
replies
142
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago
Le
• 0
1
vote
2
replies
752
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
0
votes
0
replies
28
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
1 day ago
Mirella Aurora
• 0
0
votes
3
replies
196
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
0
votes
0
replies
42
views
Warning while loading DEP package
DEP
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
0
votes
1
reply
48
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 1 day ago by
Alessia
• 0
0
votes
1
reply
80
views
Adding columns to DEXSeqResults object
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Clyde
• 0
0
votes
1
reply
56
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
ishij9717
• 0
0
votes
1
reply
52
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
09191919
• 0
0
votes
1
reply
61
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
ussarizona
• 0
0
votes
1
reply
79
views
covariate with negative and positive values
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Brynn
• 0
1
vote
2
replies
91
views
Error in champ.load(): The following specified files do not exist
ChAMP
2 days ago • updated 1 day ago
Sherin
• 0
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 1 day ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
807
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
9 days ago • updated 1 day ago
Chris
• 0
0
votes
1
reply
54
views
Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
Nina
• 0
0
votes
1
reply
79
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
quanah.hudson
• 0
3
votes
3
replies
141
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 2 days ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
0
votes
6
replies
158
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
hortense96
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 2 days ago
shepherl
3.8k
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 2 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 2 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
40
views
News:
Services
flowBeads
2 days ago
creativepeptides2018
• 0
45,551 results • Page
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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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