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bioconductor
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reset
6
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11
replies
928
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Packages don't update, but no error or warning is thrown
Bioconductor
12 weeks ago • updated 9 weeks ago
gernophil
• 0
5
votes
2
replies
729
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.2 years ago by
Victor
• 0
5
votes
1
reply
425
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
Software
written 6 months ago by
shepherl
3.8k
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.8k • written 19 months ago by
Florian Finkernagel
▴ 30
4
votes
3
replies
330
views
Bioconductor code browser time out
Bioconductor
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
Marek Gierlinski
▴ 30
3
votes
1
reply
296
views
News:
Bioconductor.org has a new look!
Bioconductor
Website
written 3 months ago by
shepherl
3.8k
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
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 8 days ago
shepherl
3.8k
2
votes
0
replies
474
views
News:
Bioconductor's Transition Away from Twitter/X
Bioconductor
5 months ago
Maria Doyle
▴ 70
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 5 months ago
Konstantinos Yeles
▴ 80
2
votes
2
replies
297
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
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
2
votes
0
replies
228
views
News:
Upholding our core values: a reminder of the Bioconductor Code of Conduct
Bioconductor
10 weeks ago
Maria Doyle
▴ 70
2
votes
1
reply
270
views
News:
"Edit" button not working
Bioconductor
Website
SupportSite
updated 12 weeks ago by
Lori
• 0 • written 3 months ago by
shepherl
3.8k
2
votes
1
reply
838
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor
biocon
limma
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
ningyuan
• 0
2
votes
11
replies
914
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 months ago by
cinzia.spagnoli
• 0
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 10 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
2
votes
4
replies
593
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
1
vote
0
replies
362
views
News:
Bioconductor Website Redesign - We Need Your Input!
Bioconductor
Website
10 months ago
shepherl
3.8k
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
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
1
vote
0
replies
208
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
7 days ago • updated 6 days ago
BioinfGuru
▴ 30
1
vote
2
replies
242
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
7 weeks ago
thomas
• 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
1
vote
1
reply
703
views
News:
Join the Community Advisory Board -- upcoming elections -- deadline Today
Bioconductor
CAB
bioconductoroversight
community
written 16 months ago by
shepherl
3.8k
1
vote
0
replies
260
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc2024
9 weeks ago • updated 7 weeks ago
shepherl
3.8k
1
vote
0
replies
566
views
News:
Last Week to Nominate for Bioc2023 Awards!
Bioconductor
Bioc2023
Recognition
Awards
11 months ago
shepherl
3.8k
1
vote
4
replies
736
views
running Bioconductor Docker images only works with versions <= 3.15
Bioconductor
8 months ago
patrick.turko
• 0
1
vote
2
replies
650
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
1
vote
4
replies
409
views
Can't post a question containing code?
Bioconductor
updated 10 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 10 weeks ago by
DS
▴ 10
0
votes
1
reply
3.4k
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
0
replies
436
views
News:
Reminder: BioC2023 in-person registration closes 19th July!
Bioconductor
BioC2023
Conference
9 months ago
Maria Doyle
▴ 70
0
votes
2
replies
909
views
MACS2 not installing
Bioconductor
7 months ago
alia.sinqua
• 0
0
votes
0
replies
575
views
News:
RNA-seq analysis with Bioconductor Carpentries workshop, Boston, Jul 31-Aug 1
Bioconductor
Event
Community
Training
11 months ago
Maria Doyle
▴ 70
0
votes
8
replies
8.5k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 5 months ago by
Marcel Ramos
690 • written 2.7 years ago by
charlotte
▴ 10
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 17 months ago by
laujihen
• 0
0
votes
6
replies
826
views
Merge 2 accounts, or delete 1 account.
Bioconductor
ALL
11 months ago • updated 10 months ago
simone.tiberi
• 0
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
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
0
votes
2
replies
2.4k
views
vmatchPattern on DNAstring set
Bioconductor
9 months ago
Avner
• 0
0
votes
0
replies
344
views
News:
May 31st is the last day to nominate for Bioc2023 Awards!
Bioconductor
Awards
Bioc2023
Recognition
11 months ago
shepherl
3.8k
0
votes
0
replies
230
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
5 months ago
Joshua
• 0
0
votes
0
replies
1.0k
views
News:
Join the Technical Advisory Board
Bioconductor
News
Organization
11 months ago
Maria Doyle
▴ 70
0
votes
0
replies
470
views
News:
Junior Developer or New Package Developer Award
Bioconductor
Recognition
Bioc2023
Awards
11 months ago
shepherl
3.8k
0
votes
1
reply
470
views
BiocManager Package installs
Bioconductor
updated 10 months ago by
shepherl
3.8k • written 10 months ago by
joseph.cerra
• 0
0
votes
0
replies
160
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
10 weeks ago
Maria Doyle
▴ 70
0
votes
7
replies
349
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
26 days ago • updated 24 days ago
needNGS
• 0
0
votes
0
replies
494
views
News:
Nominations for Bioconductor 2023 Awards!
Awards
Bioconductor
Bioc2023
Recognition
12 months ago • updated 11 months ago
shepherl
3.8k
0
votes
0
replies
71
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
14 days ago
shepherl
3.8k
50 results • Page
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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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