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0
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5
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274
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ChAMP installation issue
Cha
ChAMP
updated 22 hours ago by
shepherl
3.9k • written 9 days ago by
e1271094
• 0
0
votes
1
reply
173
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 9 days ago by
Guido Hooiveld
★ 4.0k • written 9 days ago by
aogunbaw
• 0
0
votes
2
replies
167
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 7 days ago by
zhouwanding
▴ 10 • written 10 days ago by
Seungmin
• 0
2
votes
2
replies
421
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
10 days ago • updated 5 days ago
Matthew Thornton
▴ 360
0
votes
1
reply
189
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 12 days ago by
ATpoint
★ 4.1k • written 12 days ago by
sajadahmad41454
• 0
0
votes
0
replies
90
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
12 days ago
neilzhao
▴ 30
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 13 days ago by
ATpoint
★ 4.1k • written 13 days ago by
sajadahmad41454
• 0
1
vote
2
replies
291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
13 days ago • updated 12 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
435
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
14 days ago • updated 11 days ago
sajadahmad41454
• 0
0
votes
0
replies
81
views
Treeio as.treedata function seq lenght error
treeio
14 days ago
nromerov
• 0
2
votes
2
replies
293
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
14 days ago • updated 9 days ago
zzrammal
• 0
3
votes
10
replies
500
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 12 days ago by
James W. MacDonald
66k • written 14 days ago by
Abbey
• 0
0
votes
1
reply
122
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 15 days ago by
shepherl
3.9k • written 15 days ago by
cyril.dalmasso
• 0
2
votes
1
reply
196
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 15 days ago by
James W. MacDonald
66k • written 15 days ago by
e1271094
• 0
0
votes
0
replies
102
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
15 days ago
Dinesh
• 0
3
votes
5
replies
310
views
Help with running egsea()
EGSEA
15 days ago • updated 14 days ago
Chris
▴ 10
3
votes
1
reply
158
views
How to save the DEXSeq results
DEXSeq
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Sara
• 0
2
votes
1
reply
151
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 15 days ago by
Michael Love
42k • written 16 days ago by
mat149
▴ 70
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by
Michael Love
42k • written 16 days ago by
fduguchunhui
• 0
4
votes
5
replies
348
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
16 days ago • updated 7 days ago
Chris
▴ 10
7
votes
6
replies
654
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 16 days ago by
robersy
• 0
2
votes
2
replies
240
views
fgsea significant result
fgsea
17 days ago • updated 16 days ago
Chris
▴ 10
1
vote
2
replies
411
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
Kim
• 0
2
votes
3
replies
290
views
package goseq seems to be not available on the latest version of R
goseq
updated 16 days ago by
Gordon Smyth
50k • written 18 days ago by
Patrycja
▴ 20
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Reza
• 0
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Zainab
▴ 10
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
18 days ago
Henry
▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 18 days ago by
swbarnes2
★ 1.4k • written 19 days ago by
arfranco
▴ 130
4
votes
2
replies
645
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
19 days ago • updated 15 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 19 days ago by
z_bahari
• 0
0
votes
1
reply
166
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 19 days ago by
Gordon Smyth
50k • written 19 days ago by
c53aba27
• 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
19 days ago
tholmes
• 0
0
votes
2
replies
176
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
Espresso
• 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
19 days ago
yvonneh
• 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 days ago
Ian D.
▴ 70
0
votes
1
reply
147
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 20 days ago by
4r-rtg
• 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago
kcarey
• 0
0
votes
3
replies
233
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 20 days ago by
ATpoint
★ 4.1k • written 20 days ago by
james.zhang20
• 0
1
vote
3
replies
314
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 20 days ago by
angelathuynh5
• 0
4
votes
0
replies
147
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
20 days ago
shepherl
3.9k
0
votes
0
replies
143
views
Empty table plot using plotGseaTable()
fgsea
20 days ago • updated 18 days ago
Chris
▴ 10
3
votes
4
replies
299
views
Store output of matchPWM()
biostrings
Biostrings
20 days ago • updated 8 days ago
mat149
▴ 70
0
votes
4
replies
383
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 10 days ago by
Ziliang
• 0 • written 21 days ago by
Ian D.
▴ 70
1
vote
2
replies
303
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
21 days ago • updated 20 days ago
Yveto
• 0
0
votes
3
replies
308
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by
Michael Love
42k • written 21 days ago by
HAK
• 0
3
votes
4
replies
274
views
Help with error using camera() in limma
CAMERA
limma
21 days ago
Chris
▴ 10
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 22 days ago by
Michael Love
42k • written 22 days ago by
marcusn
• 0
0
votes
0
replies
97
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
22 days ago
Maria Doyle
▴ 70
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Dev
• 0
0
votes
2
replies
174
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
22 days ago • updated 19 days ago
Aurora
• 0
179 results • Page
2 of 4
Recent ...
Replies
Comment: Slightly different count plots from R and spreadsheet
by
ATpoint
★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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