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BioConductor
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6
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11
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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
723
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
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1
reply
420
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
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written 6 months ago by
shepherl
3.8k
5
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18
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7.4k
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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
4
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3
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328
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Bioconductor code browser time out
Bioconductor
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
Marek Gierlinski
▴ 30
4
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10
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1.7k
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Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.8k • written 19 months ago by
Florian Finkernagel
▴ 30
3
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1
reply
295
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News:
Bioconductor.org has a new look!
Bioconductor
Website
written 3 months ago by
shepherl
3.8k
3
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5
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1.1k
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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
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18
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2.9k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 7 days ago
shepherl
3.8k
2
votes
2
replies
294
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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
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
1
reply
835
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
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0
replies
472
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News:
Bioconductor's Transition Away from Twitter/X
Bioconductor
5 months ago
Maria Doyle
▴ 70
2
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0
replies
227
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News:
Upholding our core values: a reminder of the Bioconductor Code of Conduct
Bioconductor
10 weeks ago
Maria Doyle
▴ 70
2
votes
11
replies
911
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Error MakeOrgPackagefromNCBI
Bioconductor
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 months ago by
cinzia.spagnoli
• 0
2
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1
reply
269
views
News:
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Bioconductor
Website
SupportSite
updated 12 weeks ago by
Lori
• 0 • written 3 months ago by
shepherl
3.8k
2
votes
5
replies
1.3k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 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 5 months ago
Konstantinos Yeles
▴ 80
2
votes
4
replies
588
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
2
replies
648
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
0
replies
565
views
News:
Last Week to Nominate for Bioc2023 Awards!
Bioconductor
Bioc2023
Recognition
Awards
11 months ago
shepherl
3.8k
1
vote
1
reply
702
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
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259
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc2024
9 weeks ago • updated 7 weeks ago
shepherl
3.8k
1
vote
1
reply
1.0k
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News:
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Bioc2022
Awards
Bioconductor
Recognition
written 2.1 years ago by
shepherl
3.8k
1
vote
4
replies
405
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
1
vote
4
replies
734
views
running Bioconductor Docker images only works with versions <= 3.15
Bioconductor
8 months ago
patrick.turko
• 0
1
vote
0
replies
199
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
6 days ago • updated 5 days ago
BioinfGuru
▴ 30
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
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
2
replies
240
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
7 weeks ago • updated 6 weeks ago
thomas
• 0
1
vote
0
replies
358
views
News:
Bioconductor Website Redesign - We Need Your Input!
Bioconductor
Website
10 months ago
shepherl
3.8k
1
vote
0
replies
492
views
News:
Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023!
Training
Bioconductor
Event
Community
News
12 months ago
Maria Doyle
▴ 70
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
435
views
News:
Reminder: BioC2023 in-person registration closes 19th July!
Bioconductor
BioC2023
Conference
9 months ago
Maria Doyle
▴ 70
0
votes
2
replies
906
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 16 months ago by
laujihen
• 0
0
votes
6
replies
824
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
2.3k
views
vmatchPattern on DNAstring set
Bioconductor
9 months ago
Avner
• 0
0
votes
0
replies
343
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
228
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
466
views
News:
Junior Developer or New Package Developer Award
Bioconductor
Recognition
Bioc2023
Awards
11 months ago
shepherl
3.8k
0
votes
1
reply
469
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
158
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
10 weeks ago
Maria Doyle
▴ 70
0
votes
7
replies
347
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
25 days ago • updated 23 days ago
needNGS
• 0
0
votes
0
replies
493
views
News:
Nominations for Bioconductor 2023 Awards!
Awards
Bioconductor
Bioc2023
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12 months ago • updated 11 months ago
shepherl
3.8k
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Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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