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0
votes
0
replies
85
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
28 days ago
Macsue
• 0
1
vote
4
replies
426
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 28 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
753
views
error in install immunedeconv
Install
updated 28 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
418
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 28 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
0
votes
2
replies
182
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
28 days ago
Gimena
• 0
0
votes
2
replies
155
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
28 days ago
Marianna
▴ 20
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 29 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
322
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 29 days ago by
s.malik
• 0
1
vote
1
reply
148
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago • updated 28 days ago
Layal
• 0
0
votes
2
replies
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 weeks ago • updated 29 days ago
w.cookson
• 0
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
29 days ago • updated 28 days ago
michelafrancesconi8
• 0
0
votes
1
reply
137
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Reeya
• 0
0
votes
4
replies
250
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
4
replies
409
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago • updated 29 days ago
Lucy
▴ 60
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 27 days ago
Bhawna
• 0
0
votes
1
reply
155
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
ja569116
• 0
0
votes
2
replies
287
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 26 days ago
fer_talavera
• 0
0
votes
2
replies
249
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 12 days ago
isaac.vock
• 0
0
votes
7
replies
383
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago • updated 29 days ago
needNGS
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 1 day ago
Chris
• 0
0
votes
4
replies
234
views
Minfi - estimatecellscount
min
minfi
updated 2 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
5
votes
25
replies
862
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
343
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 29 days ago
Gordon
• 0
6
votes
5
replies
417
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
1
vote
4
replies
438
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 12 hours ago
JKim
• 0
0
votes
7
replies
400
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 26 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
0
votes
2
replies
779
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
590
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 15 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
332
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 21 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
5.1k
views
SingleR Label.Ont
SingleR
updated 16 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 14 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 14 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
1
vote
3
replies
845
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 7 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 18 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 12 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
506
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 22 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
0
votes
2
replies
906
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 14 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
1
reply
550
views
CopywriteR output
CopywriteR
updated 26 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
3
votes
1
reply
751
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
2
replies
913
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
730
views
DESeq2 setting significant p-value
DESeq2
updated 12 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 1 day ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 18 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
204 results • Page
4 of 5
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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