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bioconductor
•
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0
votes
21
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 16 hours ago
shepherl
3.8k
5
votes
18
replies
7.4k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 3 months ago by
picasa1983
• 0 • written 2.2 years ago by
Victor
• 0
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor
ConsensusClusterPlus
updated 8 months ago by
Mehdi
• 0 • written 16 months ago by
k.wickstrom
• 0
2
votes
11
replies
891
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 10 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 months ago by
cinzia.spagnoli
• 0
6
votes
11
replies
889
views
Packages don't update, but no error or warning is thrown
Bioconductor
11 weeks ago • updated 8 weeks ago
gernophil
• 0
4
votes
10
replies
1.7k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 5 months ago by
shepherl
3.8k • written 19 months ago by
Florian Finkernagel
▴ 30
0
votes
8
replies
8.5k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 4 months ago by
Marcel Ramos
690 • written 2.7 years ago by
charlotte
▴ 10
0
votes
7
replies
312
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
18 days ago • updated 15 days ago
needNGS
• 0
0
votes
6
replies
2.1k
views
Error when Installing BioConductor Package ('affy')
Bioconductor
Install
affy
updated 5 months ago by
ATpoint
★ 4.0k • written 16 months ago by
laujihen
• 0
0
votes
6
replies
818
views
Merge 2 accounts, or delete 1 account.
Bioconductor
ALL
10 months ago
simone.tiberi
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 13 months ago by
Rebekah
• 0
0
votes
5
replies
929
views
What to whitelist in Firewall to allow downloading packages
Bioconductor
NetworkInference
updated 9 months ago by
shepherl
3.8k • written 9 months ago by
Albert
• 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 29 days ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
3
votes
5
replies
1.1k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor
Install
library
biocmanager
updated 9 months ago by
Vincent J. Carey, Jr.
6.7k • written 9 months ago by
Ndimensional
▴ 20
1
vote
4
replies
714
views
running Bioconductor Docker images only works with versions <= 3.15
Bioconductor
8 months ago
patrick.turko
• 0
2
votes
4
replies
3.7k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 9 weeks ago by
Gordon Smyth
50k • written 4.7 years ago by
sambunga094
• 0
2
votes
4
replies
573
views
Import a Bioconductor package that is only used in a vignette/.Rmd script
Bioconductor
PackageType
BiocStyle
updated 5 months ago by
shepherl
3.8k • written 5 months ago by
lavanilla44
• 0
0
votes
4
replies
723
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
11 months ago
sreeshmaraj72
• 0
0
votes
4
replies
658
views
Bioconductor installation
Bioconductor
written 3 months ago by
Akhil
• 0
1
vote
4
replies
393
views
Can't post a question containing code?
Bioconductor
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 9 weeks ago by
DS
▴ 10
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.1 years ago by
tanya
• 0
0
votes
3
replies
516
views
Support for installation and usage of TxDb.Hsapiens.UCSC.hg19.knownGene package in R version 4.2.2
Bioconductor
BiocPkgTools
5 months ago
blessybo
• 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
8.4 years ago • updated 5 months ago
Konstantinos Yeles
▴ 80
4
votes
3
replies
313
views
Bioconductor code browser time out
Bioconductor
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
Marek Gierlinski
▴ 30
0
votes
2
replies
1.3k
views
Conducting pair-wise comparison in DESeq2?
DESeq2
deseq2
biocondu
Bioconductor
RNASeq
written 14 months ago by
Hussain
• 0
0
votes
2
replies
150
views
bioconductor emailing list
Bioconductor
updated 23 days ago by
shepherl
3.8k • written 23 days ago by
1427972815
• 0
0
votes
2
replies
879
views
MACS2 not installing
Bioconductor
7 months ago
alia.sinqua
• 0
0
votes
2
replies
600
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
nilanjanamani88
• 0
1
vote
2
replies
639
views
unable to retrieve certain packages from bioconductor 3.15
Bioconductor
biocondu
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Ashton
▴ 10
0
votes
2
replies
754
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 11 months ago by
Virginie
• 0 • written 11 months ago by
gs12
• 0
5
votes
2
replies
691
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
6 months ago
Federico
▴ 10
0
votes
2
replies
836
views
News:
List of Deprecated Packages for Bioc3.17
Bioconductor
Deprecation
Devel
devel
12 months ago • updated 10 months ago
shepherl
3.8k
2
votes
2
replies
288
views
How to contact Bioconductor's test host?
Bioconductor
updated 3 months ago by
Hervé Pagès
16k • written 3 months ago by
Marek Gierlinski
▴ 30
0
votes
2
replies
1.0k
views
Bioconductor version cannot be validated
Bioconductor
updated 5 months ago by
Manuel
• 0 • written 7 months ago by
xlu.cpu
• 0
1
vote
2
replies
229
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
5 weeks ago
thomas
• 0
0
votes
2
replies
2.3k
views
vmatchPattern on DNAstring set
Bioconductor
8 months ago
Avner
• 0
0
votes
1
reply
274
views
News:
BioC2024 abstract submission is open!
BioC2024
Conference
Bioconductor
updated 4 weeks ago by
howell
• 0 • written 8 weeks ago by
Maria Doyle
▴ 70
0
votes
1
reply
202
views
Bioconductor: Won't Update to 3.18 with Default Command
Bioconductor
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 9 weeks ago by
vanbelj
▴ 30
0
votes
1
reply
579
views
bioconductor - rhdf5 is not avbauloable for bioconductor version "3.14"
Bioconductor
Install
updated 9 months ago by
Mike Smith
★ 6.5k • written 9 months ago by
Catia
• 0
0
votes
1
reply
184
views
Limitation on single file size and package size when developing Bioc package
packagedevelopment
datalimit
Bioconductor
updated 10 weeks ago by
Hervé Pagès
16k • written 10 weeks ago by
Xin Wang
• 0
1
vote
1
reply
692
views
News:
Join the Community Advisory Board -- upcoming elections -- deadline Today
Bioconductor
CAB
bioconductoroversight
community
written 16 months ago by
shepherl
3.8k
0
votes
1
reply
838
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 11 months ago by
Wei Shi
★ 3.6k • written 11 months ago by
Carlos
• 0
2
votes
1
reply
260
views
News:
"Edit" button not working
Bioconductor
Website
SupportSite
updated 10 weeks ago by
Lori
• 0 • written 3 months ago by
shepherl
3.8k
0
votes
1
reply
324
views
Advice needed on package using online databases (fails CHECK when database is down)
Bioconductor
updated 5 months ago by
shepherl
3.8k • written 5 months ago by
Marek Gierlinski
▴ 30
0
votes
1
reply
449
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression
Bioconductor
GEOquery
MethylationArrayData
9 months ago
Arianna
• 0
0
votes
1
reply
3.3k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Aytaç
• 0
0
votes
1
reply
1.2k
views
News:
BioC2023 abstract submission is now open!
presentation
BioC2023
Conference
community
Bioconductor
written 14 months ago by
Maria Doyle
▴ 70
1
vote
1
reply
1.0k
views
News:
Nominations for Bioconductor 2022 Awards!
Bioc2022
Awards
Bioconductor
Recognition
written 2.1 years ago by
shepherl
3.8k
50 results • Page
1 of 1
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Replies
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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