0
votes
0
replies
93
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
8 days ago arne.sahm • 0
0
votes
0
replies
67
views
News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
8 days ago Wolfgang Huber ★ 13k
1
vote
10
replies
365
views
Obtaining pheno data from CEL files
GEO affy
13 days ago • updated 7 days ago Kurtis • 0
0
votes
1
reply
133
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 10 days ago by 50k • written 10 days ago by • 0
1
vote
3
replies
208
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 10 days ago by 65k • written 10 days ago by • 0
1
vote
2
replies
180
views
MethylKit read issue
methylKit
updated 10 days ago by 65k • written 15 days ago by • 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 10 days ago by ▴ 10 • written 23 months ago by • 0
0
votes
4
replies
269
views
Help with design.matrix
limma
10 days ago • updated 9 days ago andrea.rodriguez-martinez13 • 0
0
votes
0
replies
113
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
10 days ago andromeda • 0
0
votes
2
replies
125
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 11 days ago by 65k • written 11 days ago by • 0
2
votes
2
replies
147
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 11 days ago by ★ 4.0k • written 11 days ago by ★ 1.5k
0
votes
1
reply
102
views
Granges regionCounts not returning the expected number of entries
methylKit
11 days ago • updated 10 days ago Modoc Kesner ▴ 10
0
votes
0
replies
72
views
flowDensity on a flowset
flowDensity
11 days ago fredrikwallberg • 0
1
vote
1
reply
139
views
DESeq2 - Missing values in count matrix
DESeq2
updated 11 days ago by 65k • written 12 days ago by • 0
7
votes
36
replies
5.4k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 12 days ago by • 0 • written 5.4 years ago by ★ 3.9k
0
votes
1
reply
171
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 12 days ago by ▴ 170 • written 12 days ago by • 0
0
votes
0
replies
64
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
12 days ago Macsue • 0
1
vote
4
replies
395
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 11 days ago by 50k • written 13 days ago by • 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 12 days ago by • 0 • written 5.2 years ago by • 0
0
votes
2
replies
720
views
error in install immunedeconv
Install
updated 12 days ago by • 0 • written 13 months ago by • 0
1
vote
6
replies
383
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 12 days ago by 41k • written 12 days ago by • 0
0
votes
2
replies
155
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
13 days ago • updated 12 days ago Gimena • 0
0
votes
2
replies
131
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
13 days ago Marianna ▴ 20
2
votes
6
replies
1.2k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 13 days ago by ▴ 170 • written 4 months ago by ▴ 10
0
votes
6
replies
269
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 5 days ago by ▴ 170 • written 13 days ago by • 0
1
vote
1
reply
123
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
14 days ago • updated 13 days ago Layal • 0
0
votes
2
replies
194
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
18 days ago • updated 13 days ago w.cookson • 0
0
votes
2
replies
138
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
14 days ago • updated 13 days ago michelafrancesconi8 • 0
0
votes
1
reply
104
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 14 days ago by 65k • written 14 days ago by • 0
0
votes
4
replies
205
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
0
votes
4
replies
375
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
15 days ago • updated 14 days ago Lucy ▴ 60
0
votes
1
reply
85
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 14 days ago by 65k • written 15 days ago by • 0
0
votes
2
replies
146
views
How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
15 days ago • updated 14 days ago Seongsu • 0
0
votes
2
replies
147
views
Gene Ontology doubt
microbiomeExplorer
15 days ago • updated 11 days ago Bhawna • 0
0
votes
1
reply
141
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 14 days ago by 41k • written 17 days ago by ▴ 10
0
votes
1
reply
120
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 14 days ago by 65k • written 15 days ago by • 0
0
votes
2
replies
249
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
15 days ago • updated 10 days ago fer_talavera • 0
0
votes
1
reply
186
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
updated 7 days ago by ★ 3.6k • written 15 days ago by • 0
0
votes
7
replies
299
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
16 days ago • updated 14 days ago needNGS • 0
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
17 days ago • updated 8 days ago Chris • 0
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
0
votes
2
replies
153
views
Minfi - estimatecellscount
min minfi
17 days ago clacarion • 0
0
votes
0
replies
85
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
18 days ago feather-W • 0
0
votes
0
replies
81
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
18 days ago Ankit ▴ 20
0
votes
6
replies
297
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 17 days ago by 50k • written 18 days ago by • 0
1
vote
5
replies
276
views
fgsea fork
fgsea
updated 17 days ago by 65k • written 18 days ago by • 0
0
votes
1
reply
129
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
0
replies
73
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
19 days ago Pierre Lindenbaum ▴ 10
2
votes
8
replies
467
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 19 days ago by 50k • written 20 days ago by • 0
0
votes
1
reply
105
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 19 days ago by 65k • written 19 days ago by • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: what is the sampleFiles by James W. MacDonald 65k
I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.
Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
United States, just now
France, 2 minutes ago
France, 3 minutes ago
United States, 7 minutes ago
UPF, Barcelona, Spain, 8 minutes ago
Traffic: 764 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6