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Votes
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by
Maryam.sed1400
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 15 days ago
shepherl
3.9k
1
vote
12
replies
2.4k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 180 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 8 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
luis.franco
• 0
1
vote
11
replies
3.5k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
2
votes
11
replies
942
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 7 months ago by
cinzia.spagnoli
• 0
6
votes
11
replies
1.0k
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 11 weeks ago
gernophil
• 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3.3 years ago by
Alberto
• 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
1
vote
11
replies
1.0k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 6 months ago by
Michael Love
42k • written 6 months ago by
cm15245
• 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 14 months ago by
pedro-marra
▴ 10
0
votes
11
replies
743
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
mico
• 0
9
votes
11
replies
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 7 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
3
votes
11
replies
2.5k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
11 months ago
Anna
▴ 20
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
alexia.brunel
• 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
0
votes
11
replies
2.8k
views
edgeR contrasts
edgeR
updated 8 months ago by
James W. MacDonald
65k • written 20 months ago by
ignadb
• 0
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
0
votes
11
replies
2.1k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.7 years ago by
mike Ad.
▴ 30
2
votes
10
replies
1.3k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
15753563659
▴ 50
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 18 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 17 months ago by
Alexandros
• 0
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.9k • written 19 months ago by
Florian Finkernagel
▴ 30
10
votes
10
replies
7.0k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 6 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
3
votes
10
replies
2.8k
views
error in package GenVisR while installing
GenVisR
GenVis
updated 5 months ago by
zlskidmore
▴ 30 • written 21 months ago by
abhisikta
• 0
0
votes
10
replies
819
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 9 weeks ago
ScafioRuo
• 0
2
votes
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
2
votes
10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by
Michael Love
42k • written 5.7 years ago by
andrebolerbarros
▴ 20
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 23 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
0
votes
10
replies
844
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
cjag
• 0
1
vote
10
replies
458
views
Obtaining pheno data from CEL files
GEO
affy
5 weeks ago • updated 28 days ago
Kurtis
• 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by
dbunis
▴ 10 • written 8 months ago by
nina.hahn
▴ 10
6
votes
9
replies
770
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
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago • updated 3 months ago
Luca
• 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.9 years ago by
stan
• 0
2
votes
9
replies
1.8k
views
How to load fasta file with openPrimeR?
openPrimeR
written 3.2 years ago by
marongiu.luigi
• 0
0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin
DESeq2
updated 6 months ago by
yujin
▴ 10 • written 22 months ago by
Weiqian
▴ 10
0
votes
9
replies
845
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
4
votes
9
replies
404
views
Memory errors using read.bismark?
dmrseq
bsseq
26 days ago • updated 27 minutes ago
Juan Higareda
• 0
1
vote
9
replies
888
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 9 months ago by
Michael Love
42k • written 10 months ago by
Matteo
• 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
8 months ago
15753563659
▴ 50
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 19 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
9
replies
850
views
estimateDisp() error
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
ASNbioinf
• 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
0
votes
9
replies
855
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago
mjd275
• 0
1,749 results • Page
2 of 35
Recent ...
Replies
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark?
by
Juan Higareda
• 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance
by
James W. MacDonald
65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip
by
James W. MacDonald
65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Answer: Recovering my account credentials on Bioconductor
by
shepherl
3.9k
As we will need to exchange some information can you please contact me at bioconductorcoreteam@gmail.com and I can better assist you. Che…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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