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Ensemble site connection error
biomaRt
31 minutes ago
Makoto
• 0
1
vote
4
replies
1.2k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 1 hour ago by
Leonardo Collado Torres
▴ 870 • written 3.6 years ago by
maleknias
• 0
0
votes
1
reply
60
views
News:
Bioconductor 3.13 New Package Submission Deadline
release
Submission
newpackage
Release
Deadline
8 days ago • updated 14 hours ago
shepherl
2.6k
0
votes
0
replies
26
views
DiffBind
ATACSeq
DiFFBind
17 hours ago
Riba Michela
▴ 80
2
votes
3
replies
80
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
updated 4 hours ago by
Gordon Smyth
42k • written 1 day ago by
Antonio M.
• 0
0
votes
2
replies
57
views
GenomeInfoDb’ could not be loaded or installed
GenomeInfoDbData
updated 1 day ago by
Hervé Pagès
14k • written 2 days ago by
ettore64
• 0
0
votes
2
replies
134
views
Error: package or namespace load failed for ‘org.Hs.eg.db’:
$operator
atomicvectors
updated 1 day ago by
ramashan
• 0 • written 4 days ago by
dazhiruoyujingjie
• 0
1
vote
2
replies
59
views
DESeq2 for TRAP-seq methods
DESeq2
TRAP-seq
2 days ago • updated 1 day ago
marypiper
• 0
1
vote
2
replies
63
views
DESeq2 unmix function
DESeq2
1 day ago • updated 16 hours ago
Sam
▴ 10
1
vote
3
replies
76
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
1 day ago
dantasezequiel1
• 0
0
votes
0
replies
18
views
Job:
Bioinformatician / Software Developer with Flow Cytometry experience.
JobPosting
Flow-Cytometry
1 day ago
Martin
• 0
0
votes
1
reply
43
views
Sorting columns in pheatmap
pheatmap
updated 1 day ago by
Chris Seidel
▴ 70 • written 1 day ago by
Linda
• 0
0
votes
6
replies
1.0k
views
clusterProfiler: different runs return different results for gse functions
clusterprofiler
updated 1 day ago by
josep
• 0 • written 3.6 years ago by
ssv
• 0
0
votes
2
replies
52
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
1 day ago
waiyin0923
• 0
3
votes
5
replies
87
views
unable to forge custom BSgenome after update
BSgenome
updated 1 day ago by
Hervé Pagès
14k • written 1 day ago by
Chris Seidel
▴ 70
0
votes
0
replies
21
views
Mass spec intensity difference
xcms
1 day ago
Phytochem
• 0
0
votes
0
replies
24
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
2 days ago
Thomas.H.Hampton
• 0
0
votes
1
reply
38
views
Extract data from pair files
nimblegen
pair
updated 2 days ago by
James W. MacDonald
56k • written 2 days ago by
Dhanya
• 0
0
votes
0
replies
31
views
News:
Support Site Bioconductor Award
recognition
awards
bioc2021
Bioconductor
2 days ago
shepherl
2.6k
2
votes
3
replies
78
views
Which DESeq normalization method?
DESeq2
updated 2 days ago by
Michael Love
32k • written 2 days ago by
save
• 0
0
votes
2
replies
61
views
Error running ExperimentHubData::makeExperimentHubMetadata on Windows 10
BiocCheck
updated 2 days ago by
shepherl
2.6k • written 4 days ago by
wewolski
▴ 10
1
vote
2
replies
91
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
updated 2 days ago by
shepherl
2.6k • written 6 days ago by
Nicol
• 0
4
votes
4
replies
142
views
How to apply limma-trend or voom to batch corrected single cell data? (non-integer and negative values included)
MNNCorrect
scMerge
limma-trend
6 days ago • updated 2 days ago
hainct
• 0
0
votes
1
reply
59
views
Correcting partially penetrant batch effect
DESeq2
updated 3 days ago by
Michael Love
32k • written 4 days ago by
swbarnes2
▴ 680
2
votes
1
reply
66
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3 days ago by
Michael Love
32k • written 3 days ago by
Pufall, Miles A
▴ 30
3
votes
2
replies
111
views
Error Loading "org.Dm.eg.db" package
r
org.Dm.eg.db
updated 3 days ago by
Chris Seidel
▴ 70 • written 3 days ago by
Amanda
▴ 10
3
votes
2
replies
63
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
3 days ago
Assa Yeroslaviz
★ 1.5k
40
votes
29
replies
2.9k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 1 day ago by
Kevin Ushey
▴ 110 • written 10 days ago by
Arun
▴ 150
0
votes
0
replies
35
views
PCA theoretical question for applied case
pcaMethods
3 days ago
Gero
• 0
2
votes
2
replies
265
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
4 days ago
Jack
• 0
0
votes
0
replies
35
views
motifBreakR error with custom BSgenome
GenomeInfoDb
motifbreakR
4 days ago • updated 11 hours ago
Chris Seidel
▴ 70
0
votes
11
replies
248
views
Aspli: error with gbCounts
Aspli
ASpli
4 weeks ago • updated 1 day ago
jbono
• 0
1
vote
1
reply
54
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 5 days ago by
Michael Love
32k • written 6 days ago by
l.troxler
▴ 10
1
vote
8
replies
148
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 3 days ago by
Kevin Blighe
2.8k • written 6 days ago by
dorina.jamniczky
• 0
0
votes
9
replies
616
views
Thoughts on computer purchase
computer
updated 5 days ago by
Gordon Smyth
42k • written 15.0 years ago by
Lance Palmer
▴ 60
2
votes
2
replies
88
views
Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 3 days ago by
Kevin Blighe
2.8k • written 6 days ago by
Javier
• 0
0
votes
1
reply
32
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 5 days ago by
Anaysha
• 0 • written 6 days ago by
cviner
• 0
0
votes
6
replies
124
views
Sample quality weights for RNA-seq
DESeq2
limma
weight
7 days ago • updated 4 days ago
Naomi Altman
★ 6.0k
1
vote
2
replies
153
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
16 days ago • updated 2 days ago
mwong043
• 0
1
vote
2
replies
63
views
Warning with the example of GSEA
fgsea
fgse
updated 6 days ago by
Kevin Blighe
2.8k • written 6 days ago by
julie.hardy
• 0
3
votes
2
replies
49
views
Biomart Errors
biomaRt
6 days ago
Dr. Connie Brett
▴ 10
0
votes
2
replies
96
views
DepMap copy number
software error
depmap
updated 3 days ago by
E
• 0 • written 6 months ago by
DannyM
• 0
0
votes
1
reply
50
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
updated 6 days ago by
James W. MacDonald
56k • written 6 days ago by
Laura
• 0
0
votes
1
reply
45
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 6 days ago by
Mike Smith
★ 4.9k • written 6 days ago by
Jeremy
• 0
2
votes
1
reply
43
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 6 days ago by
Kevin Blighe
2.8k • written 6 days ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
76
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
6 days ago • updated 2 days ago
xiaofeiwang18266
▴ 20
0
votes
0
replies
21
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
6 days ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
48
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 5 days ago by
Sam
▴ 10 • written 6 days ago by
ikumar2000
• 0
1
vote
15
replies
219
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
8 days ago • updated 5 days ago
demisa
• 0
1
vote
4
replies
94
views
EnhancedVolcano plot with colCustom
EnhancedVolcano
7 days ago • updated 2 days ago
Neeraja Vegesna
▴ 10
40,587 results • Page
1 of 812
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Replies
Comment: lpsymphony compilation trouble
by
Dario Strbenac
★ 1.5k
This problem still exists in 2021 and deleting `pkgconfig` folder is still the workaround. May it be fixed once and for all in the package …
Comment: NA values of count matrix in class DESeqDataSet
by
Leonardo Collado Torres
▴ 870
Nice, thanks for the answer! Best, Leo
Comment: Pipeline for an Anova-like analysis in edgeR
by
Gordon Smyth
42k
There is no way to combine fold-change thresholding with an F-test. Fold-changes can only be associated with individual t-tests. So if you …
Answer: NA values of count matrix in class DESeqDataSet
by
Amit
▴ 10
I got trapped in a similar problem but found a solution by myself. In my case, extra space after count matrix data was the reason for this …
Comment: Couldn't load org.Hs.eg.db
by
Will
• 0
This worked for me: remotes::install_version("RSQLite", version = "2.2.5") and then just library(org.Hs.eg.db) with R version of 4.0.3
Votes
Answer: NA values of count matrix in class DESeqDataSet
Answer: Couldn't load org.Hs.eg.db
Answer: Pipeline for an Anova-like analysis in edgeR
Answer: Pipeline for an Anova-like analysis in edgeR
Answer: DESeq2 unmix function
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