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Votes
3
votes
7
replies
907
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
8 months ago
casco
▴ 10
2
votes
4
replies
1.3k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 7 months ago by
Matt Eldridge
• 0 • written 7 months ago by
r.murakami
• 0
0
votes
6
replies
291
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 14 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
arfranco
▴ 130
0
votes
2
replies
532
views
SPIAT for HALO manual phenotype entry
PHENOTYPE
SPIAT
HALO
updated 9 months ago by
yuzhou.feng
• 0 • written 10 months ago by
Jack
• 0
0
votes
2
replies
647
views
Fluidigm Data Batch Correction
sva
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Khushbu
• 0
0
votes
2
replies
934
views
Rgraphviz installation: DLL problem?
Rgraphviz
Rgraphviz
written 14.3 years ago by
Gustavo Lacerda
▴ 10
0
votes
3
replies
807
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 9 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 4 weeks ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
2
votes
7
replies
4.8k
views
Installing Local packages in Bioconductor
package
updated 9 months ago by
Boxun
• 0 • written 2.0 years ago by
BioC123
• 0
0
votes
6
replies
363
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 5 weeks ago by
Tim Peters
▴ 180 • written 6 weeks ago by
s.malik
• 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
1
vote
6
replies
522
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Lucy
▴ 60
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
9 months ago
15753563659
▴ 50
3
votes
4
replies
505
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 9 days ago by
Mike Smith
★ 6.5k • written 12 days ago by
robersy
• 0
0
votes
5
replies
716
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 11 months ago by
Lillian
• 0
2
votes
3
replies
1.2k
views
Problem with function combine regarding merging two data frames based on their common rows
bioconductor
merge data frames
combine
biocgenerics
8.5 years ago • updated 6 months ago
Konstantinos Yeles
▴ 80
1
vote
5
replies
600
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago
ilaria.maurizio
• 0
2
votes
2
replies
211
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
sansan
• 0
2
votes
1
reply
291
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago
mat149
▴ 70
0
votes
2
replies
1.1k
views
error when using M-values in ChAMP
ChAMP
updated 7 weeks ago by
hortense96
• 0 • written 6.3 years ago by
a.mcneill
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 29 days ago by
Garrett
• 0 • written 9.2 years ago by
brohawndg
▴ 150
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.3 years ago by
Carolina
• 0
1
vote
3
replies
911
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 11 months ago by
lauryfriese932
• 0 • written 12 months ago by
shashank
• 0
0
votes
2
replies
836
views
R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 10 months ago by
Michael Love
42k • written 10 months ago by
ikpa_p123
• 0
5
votes
19
replies
6.0k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
7
votes
3
replies
1.2k
views
work shops/summer schools
written 20.2 years ago by
Miroslava Cuperlovic-Culf
▴ 50
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by
Amruta
• 0 • written 5.3 years ago by
r.tor
• 0
0
votes
9
replies
869
views
estimateDisp() error
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
ASNbioinf
• 0
0
votes
2
replies
875
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 22 hours ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
1
vote
7
replies
1.6k
views
enrichGOgradient color change
clusterProfiler
updated 8 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 months ago by
inna.gur
• 0
0
votes
2
replies
382
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 10 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Suvi
• 0
0
votes
5
replies
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by
Rory Stark
★ 5.2k • written 4.3 years ago by
Jim
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 25 days ago
shepherl
3.9k
0
votes
2
replies
377
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
bas_work
▴ 30
1
vote
5
replies
882
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
9 months ago
duez.tolga
• 0
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by
hasse.bossenbroek
• 0
6
votes
9
replies
859
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 3 months ago by
alexander3
• 0 • written 3 months ago by
Amparo
• 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Bo
• 0
3
votes
4
replies
270
views
Store output of matchPWM()
biostrings
Biostrings
16 days ago • updated 4 days ago
mat149
▴ 70
1
vote
2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 12 months ago by
brukti
• 0 • written 8.7 years ago by
akridgerunner
▴ 30
0
votes
3
replies
480
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
0
votes
4
replies
919
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
42k • written 9 months ago by
hanc
• 0
1
vote
2
replies
473
views
Assess fit of variance prior
limma
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Frederik Ziebell
▴ 20
5
votes
5
replies
468
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago
baptiste
▴ 20
0
votes
2
replies
188
views
bioconductor emailing list
Bioconductor
updated 7 weeks ago by
shepherl
3.9k • written 7 weeks ago by
1427972815
• 0
2
votes
28
replies
4.5k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
65k • written 17 months ago by
Manmohit
▴ 10
1,738 results • Page
4 of 35
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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