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Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
11 days ago
arne.sahm
• 0
0
votes
0
replies
73
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
11 days ago
Wolfgang Huber
★ 13k
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 11 days ago
Chris
• 0
0
votes
4
replies
281
views
Help with design.matrix
limma
13 days ago • updated 12 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
139
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
avery
• 0
1
vote
3
replies
220
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
108
views
Granges regionCounts not returning the expected number of entries
methylKit
14 days ago • updated 13 days ago
Modoc Kesner
▴ 10
1
vote
2
replies
190
views
MethylKit read issue
methylKit
updated 13 days ago by
James W. MacDonald
65k • written 18 days ago by
CHEN
• 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 13 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
1
reply
528
views
CopywriteR output
CopywriteR
updated 13 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
18 days ago • updated 13 days ago
fer_talavera
• 0
0
votes
0
replies
122
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
13 days ago
andromeda
• 0
0
votes
2
replies
132
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
158
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 14 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Dario Strbenac
★ 1.5k
2
votes
5
replies
993
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 14 days ago by
damian.szk
▴ 80 • written 4 months ago by
Abhishek
• 0
1
vote
4
replies
398
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 14 days ago by
Gordon Smyth
50k • written 16 days ago by
jari.karppinen
• 0
5
votes
25
replies
781
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 24 days ago by
Jitendra
▴ 10
0
votes
0
replies
77
views
flowDensity on a flowset
flowDensity
14 days ago
fredrikwallberg
• 0
0
votes
2
replies
156
views
Gene Ontology doubt
microbiomeExplorer
18 days ago • updated 14 days ago
Bhawna
• 0
1
vote
1
reply
145
views
DESeq2 - Missing values in count matrix
DESeq2
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
Hong Thu
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 15 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
189
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 15 days ago by
Tim Peters
▴ 170 • written 15 days ago by
Kim
• 0
0
votes
0
replies
70
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
15 days ago
Macsue
• 0
1
vote
6
replies
392
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 15 days ago by
Michael Love
41k • written 15 days ago by
RL
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 15 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
728
views
error in install immunedeconv
Install
updated 15 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
0
votes
2
replies
162
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago • updated 15 days ago
Gimena
• 0
0
votes
2
replies
139
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
16 days ago
Marianna
▴ 20
0
votes
2
replies
142
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
17 days ago • updated 16 days ago
michelafrancesconi8
• 0
1
vote
1
reply
128
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
17 days ago • updated 16 days ago
Layal
• 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 16 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
0
votes
2
replies
305
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
27 days ago • updated 16 days ago
Gordon
• 0
0
votes
4
replies
215
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
Aidan
• 0
0
votes
2
replies
205
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
21 days ago • updated 16 days ago
w.cookson
• 0
0
votes
4
replies
385
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
18 days ago • updated 17 days ago
Lucy
▴ 60
0
votes
1
reply
126
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
ja569116
• 0
0
votes
1
reply
111
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Reeya
• 0
0
votes
7
replies
319
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
19 days ago • updated 17 days ago
needNGS
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 17 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
0
votes
2
replies
153
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
18 days ago • updated 17 days ago
Seongsu
• 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
0
votes
1
reply
90
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
Leyre
• 0
0
votes
1
reply
146
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 17 days ago by
Michael Love
41k • written 20 days ago by
saadmurtazakhan
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 18 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 18 days ago by
isaac.vock
• 0 • written 7.8 years ago by
Jon Manning
▴ 90
0
votes
3
replies
307
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
3
votes
5
replies
325
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 19 days ago by
Gordon Smyth
50k • written 21 days ago by
Fabian
• 0
0
votes
2
replies
688
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
0
votes
6
replies
302
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 21 days ago by
Faisal
• 0
45,548 results • Page
3 of 911
Recent ...
Replies
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
Or that. ;-D
Answer: Error retrieving ensembl gene id using biomaRt...
by
Mike Smith
★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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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