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2
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tximeta Error in UseMethod("filter_")
tximeta
10 minutes ago
Pufall, Miles A
▴ 20
0
votes
0
replies
11
views
Correcting partially penetrant batch effect
DESeq2
6 hours ago • updated 5 hours ago
swbarnes2
▴ 680
0
votes
1
reply
32
views
How to apply limma-trend or voom to batch corrected single cell data? (non-integer and negative values included)
MNNCorrect
scMerge
limma-trend
updated 6 hours ago by
Gordon Smyth
42k • written 2 days ago by
hainct
• 0
0
votes
1
reply
41
views
Error: package or namespace load failed for ‘org.Hs.eg.db’:
$operator
atomicvectors
updated 16 hours ago by
James W. MacDonald
56k • written 20 hours ago by
dazhiruoyujingjie
• 0
2
votes
2
replies
45
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
19 hours ago • updated 16 hours ago
Jack
• 0
0
votes
0
replies
22
views
Error running ExperimentHubData::makeExperimentHubMetadata on Windows 10
BiocCheck
22 hours ago
wewolski
▴ 10
0
votes
0
replies
18
views
motifBreakR error with custom BSgenome and snps.from.file function
GenomeInfoDb
motifbreakR
1 day ago • updated 6 hours ago
Chris Seidel
▴ 50
0
votes
10
replies
210
views
Aspli: error with gbCounts
Aspli
ASpli
updated 1 day ago by
achernomoretz
• 0 • written 26 days ago by
jbono
• 0
1
vote
1
reply
41
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 1 day ago by
Michael Love
32k • written 2 days ago by
l.troxler
▴ 10
1
vote
6
replies
94
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 1 day ago by
Kevin Blighe
2.8k • written 2 days ago by
dorina.jamniczky
• 0
0
votes
9
replies
605
views
Thoughts on computer purchase
computer
updated 1 day ago by
Gordon Smyth
42k • written 15.0 years ago by
Lance Palmer
▴ 60
2
votes
5
replies
72
views
Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 1 day ago by
Marcel Ramos
500 • written 2 days ago by
Javier
• 0
0
votes
1
reply
21
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 1 day ago by
Anaysha
• 0 • written 2 days ago by
cviner
• 0
0
votes
6
replies
98
views
Sample quality weights for RNA-seq
DESeq2
limma
weight
3 days ago • updated 13 hours ago
Naomi Altman
★ 6.0k
1
vote
2
replies
108
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
12 days ago • updated 2 days ago
mwong043
• 0
1
vote
1
reply
40
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
updated 2 days ago by
Sina
▴ 10 • written 2 days ago by
Nicol
• 0
1
vote
2
replies
43
views
Warning with the example of GSEA
fgsea
fgse
updated 2 days ago by
Kevin Blighe
2.8k • written 2 days ago by
julie.hardy
• 0
3
votes
2
replies
34
views
Biomart Errors
biomaRt
2 days ago
Dr. Connie Brett
▴ 10
0
votes
1
reply
81
views
DepMap copy number
software error
depmap
updated 2 days ago by
Laurent Gatto
1.5k • written 6 months ago by
DannyM
• 0
0
votes
1
reply
34
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
updated 2 days ago by
James W. MacDonald
56k • written 2 days ago by
Laura
• 0
0
votes
1
reply
33
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 2 days ago by
Mike Smith
★ 4.9k • written 2 days ago by
Jeremy
• 0
2
votes
1
reply
27
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 2 days ago by
Kevin Blighe
2.8k • written 2 days ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
46
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
updated 1 day ago by
Kevin Blighe
2.8k • written 2 days ago by
xiaofeiwang18266
▴ 20
0
votes
0
replies
13
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
2 days ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
39
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 1 day ago by
Sam
▴ 10 • written 3 days ago by
ikumar2000
• 0
1
vote
15
replies
166
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
4 days ago • updated 1 day ago
demisa
• 0
0
votes
1
reply
47
views
EnhancedVolcano plot with colCustom
EnhancedVolcano
updated 3 days ago by
Kevin Blighe
2.8k • written 3 days ago by
neeraja149vegesna
• 0
0
votes
2
replies
76
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
3 days ago
Kate
• 0
1
vote
1
reply
40
views
Enhanced Volcano Plot Controlling Color Layers
EnhancedVolcano
3 days ago
dk0319
• 0
4
votes
2
replies
64
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 3 days ago by
James W. MacDonald
56k • written 3 days ago by
Gero
• 0
0
votes
0
replies
23
views
Missing sample
OSAT
3 days ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
51
views
Query regarding edgeR and limma
limma
readDGE
edgeR
updated 3 days ago by
James W. MacDonald
56k • written 4 days ago by
abhisekdey061
• 0
1
vote
0
replies
27
views
News:
Terra / AnVIL R / Bioconductor Popup Workshops
AnVIL
workshop
Bioconductor
Terra
3 days ago
shepherl
2.6k
0
votes
0
replies
21
views
News:
Bioconductor Release 3.12 and Bioconductor Devel 3.13 Code Freeze Deadlines!
deadline
Bioconductor
devel
release
3 days ago
shepherl
2.6k
0
votes
0
replies
28
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
3 days ago
hele7
▴ 20
0
votes
0
replies
28
views
Job:
Biostatistics Research Associate, York, UK
QTL
fourier
TimeSeriesExperiment
timecoursedata
3 days ago
Daphne
• 0
0
votes
0
replies
35
views
How can I correctly normalize RNA--seq data and find DEGs in complicated data set with ImpluseDE2?
ImpluseDE2
3 days ago
MU
• 0
1
vote
1
reply
49
views
simplifyEnrichment install error
package
Rversion
Install
simplifyEnrichment
updated 3 days ago by
shepherl
2.6k • written 3 days ago by
ch_el
▴ 10
4
votes
12
replies
646
views
Couldn't load org.Hs.eg.db
org.Hs.eg.db
updated 1 day ago by
R
• 0 • written 4 days ago by
Chen
▴ 20
3
votes
3
replies
78
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 3 days ago by
Michael Love
32k • written 4 days ago by
Tom
• 0
0
votes
10
replies
155
views
Problem with estimateSizeFactors due to avgTxLength
DESeq2
4 days ago • updated 1 day ago
Mark
• 0
39
votes
26
replies
1.8k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 22 hours ago by
Hao Zhang
• 0 • written 6 days ago by
Arun
▴ 150
0
votes
0
replies
36
views
News:
Nominations for Bioconductor 2021 Awards!
Awards
Recognition
Bioconductor
Bioc2021
4 days ago
shepherl
2.6k
0
votes
0
replies
33
views
News:
Bioconductor 3.13 New Package Submission Deadline
release
Submission
newpackage
Release
Deadline
4 days ago
shepherl
2.6k
0
votes
0
replies
31
views
News:
Bioconductor Release 3.13 Schedule
Release
release
5 days ago • updated 4 days ago
shepherl
2.6k
1
vote
1
reply
51
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 4 days ago by
Michael Love
32k • written 5 days ago by
xiaofeiwang18266
▴ 20
0
votes
2
replies
58
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta
BiocFileCache
updated 4 days ago by
Michael Love
32k • written 5 days ago by
judith.risse
• 0
0
votes
0
replies
55
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl
minfi
5 days ago
jefflincoln4
• 0
4
votes
4
replies
97
views
DESeq2 two conditions with interaction
DESeq2
updated 3 days ago by
swbarnes2
▴ 680 • written 5 days ago by
mboeck
• 0
0
votes
2
replies
246
views
News:
List of Deprecated Packages for Bioc3.13
Workflow
Software
Deprecation
ExperimentData
4 months ago • updated 5 days ago
shepherl
2.6k
40,568 results • Page
1 of 812
Recent ...
Replies
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
by
Gordon Smyth
42k
If you have applied mnnCorrect, then the output is already on the log-expression scale so you would directly enter standard limma pipelines…
Comment: Error: package or namespace load failed for ‘org.Mm.eg.db':
by
Jack
• 0
It worked! Brilliant. Thanks so much!
Answer: Error: package or namespace load failed for ‘org.Hs.eg.db’:
by
James W. MacDonald
56k
It’s Rstudio. https://github.com/rstudio/rstudio/issues/9219 You can try the fix proposed by Kevin Ushey in that bug report, or run R fr…
Answer: Error: package or namespace load failed for ‘org.Mm.eg.db':
by
James W. MacDonald
56k
It’s Rstudio. https://github.com/rstudio/rstudio/issues/9219 You can try the fix proposed by Kevin Ushey in that bug report, or run R fr…
Comment: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
by
Hao Zhang
• 0
Restarting works for me.
Votes
Answer: Error: package or namespace load failed for ‘org.Mm.eg.db':
Answer: Error: package or namespace load failed for ‘org.Mm.eg.db':
Couldn't load org.Hs.eg.db
Comment: Error following instructions of CBioportal R-workshop example 2
Comment: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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