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0
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8
views
DiffBind
ATACSeq
DiFFBind
1 hour ago
Riba Michela
▴ 80
0
votes
1
reply
43
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
updated 3 hours ago by
Gordon Smyth
42k • written 18 hours ago by
Antonio M.
• 0
0
votes
2
replies
50
views
GenomeInfoDb’ could not be loaded or installed
GenomeInfoDbData
updated 12 hours ago by
Hervé Pagès
14k • written 1 day ago by
ettore64
• 0
0
votes
2
replies
112
views
Error: package or namespace load failed for ‘org.Hs.eg.db’:
$operator
atomicvectors
updated 16 hours ago by
ramashan
• 0 • written 4 days ago by
dazhiruoyujingjie
• 0
1
vote
2
replies
56
views
DESeq2 for TRAP-seq methods
DESeq2
TRAP-seq
1 day ago • updated 13 hours ago
marypiper
• 0
0
votes
1
reply
37
views
DESeq2 unmix function
DESeq2
updated 18 hours ago by
Michael Love
32k • written 18 hours ago by
Sam
▴ 10
1
vote
3
replies
60
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
20 hours ago • updated 19 hours ago
dantasezequiel1
• 0
0
votes
0
replies
15
views
Job:
Bioinformatician / Software Developer with Flow Cytometry experience.
JobPosting
Flow-Cytometry
19 hours ago
Martin
• 0
0
votes
1
reply
33
views
Sorting columns in pheatmap
pheatmap
updated 11 hours ago by
Chris Seidel
▴ 70 • written 21 hours ago by
Linda
• 0
0
votes
6
replies
1.0k
views
clusterProfiler: different runs return different results for gse functions
clusterprofiler
updated 22 hours ago by
josep
• 0 • written 3.6 years ago by
ssv
• 0
0
votes
2
replies
42
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
1 day ago • updated 18 hours ago
waiyin0923
• 0
3
votes
5
replies
73
views
unable to forge custom BSgenome after update
BSgenome
updated 11 hours ago by
Hervé Pagès
14k • written 1 day ago by
Chris Seidel
▴ 70
0
votes
0
replies
18
views
Mass spec intensity difference
xcms
1 day ago
Phytochem
• 0
0
votes
0
replies
22
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
1 day ago
Thomas.H.Hampton
• 0
0
votes
1
reply
36
views
Extract data from pair files
nimblegen
pair
updated 1 day ago by
James W. MacDonald
56k • written 2 days ago by
Dhanya
• 0
0
votes
0
replies
26
views
News:
Support Site Bioconductor Award
recognition
awards
bioc2021
Bioconductor
1 day ago
shepherl
2.6k
2
votes
3
replies
68
views
Which DESeq normalization method?
DESeq2
updated 1 day ago by
Michael Love
32k • written 1 day ago by
save
• 0
0
votes
2
replies
58
views
Error running ExperimentHubData::makeExperimentHubMetadata on Windows 10
BiocCheck
updated 1 day ago by
shepherl
2.6k • written 4 days ago by
wewolski
▴ 10
1
vote
2
replies
85
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
updated 1 day ago by
shepherl
2.6k • written 5 days ago by
Nicol
• 0
4
votes
4
replies
132
views
How to apply limma-trend or voom to batch corrected single cell data? (non-integer and negative values included)
MNNCorrect
scMerge
limma-trend
5 days ago • updated 1 day ago
hainct
• 0
0
votes
1
reply
53
views
Correcting partially penetrant batch effect
DESeq2
updated 2 days ago by
Michael Love
32k • written 3 days ago by
swbarnes2
▴ 680
2
votes
1
reply
62
views
tximeta Error in UseMethod("filter_")
tximeta
updated 2 days ago by
Michael Love
32k • written 3 days ago by
Pufall, Miles A
▴ 30
3
votes
2
replies
100
views
Error Loading "org.Dm.eg.db" package
r
org.Dm.eg.db
updated 2 days ago by
Chris Seidel
▴ 70 • written 2 days ago by
Amanda
▴ 10
3
votes
2
replies
55
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
3 days ago • updated 2 days ago
Assa Yeroslaviz
★ 1.5k
40
votes
29
replies
2.7k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 13 hours ago by
Kevin Ushey
▴ 110 • written 9 days ago by
Arun
▴ 150
0
votes
0
replies
33
views
PCA theoretical question for applied case
pcaMethods
2 days ago
Gero
• 0
2
votes
2
replies
218
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
3 days ago
Jack
• 0
0
votes
0
replies
30
views
motifBreakR error with custom BSgenome and snps.from.file function
GenomeInfoDb
motifbreakR
4 days ago • updated 17 hours ago
Chris Seidel
▴ 70
0
votes
11
replies
241
views
Aspli: error with gbCounts
Aspli
ASpli
29 days ago • updated 18 hours ago
jbono
• 0
1
vote
1
reply
51
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 4 days ago by
Michael Love
32k • written 5 days ago by
l.troxler
▴ 10
1
vote
8
replies
142
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 2 days ago by
Kevin Blighe
2.8k • written 6 days ago by
dorina.jamniczky
• 0
0
votes
9
replies
615
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
85
views
Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 2 days ago by
Kevin Blighe
2.8k • written 6 days ago by
Javier
• 0
0
votes
1
reply
28
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 5 days ago by
Anaysha
• 0 • written 5 days ago by
cviner
• 0
0
votes
6
replies
119
views
Sample quality weights for RNA-seq
DESeq2
limma
weight
6 days ago • updated 3 days ago
Naomi Altman
★ 6.0k
1
vote
2
replies
144
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
15 days ago • updated 1 day ago
mwong043
• 0
1
vote
2
replies
60
views
Warning with the example of GSEA
fgsea
fgse
updated 5 days ago by
Kevin Blighe
2.8k • written 6 days ago by
julie.hardy
• 0
3
votes
2
replies
44
views
Biomart Errors
biomaRt
5 days ago
Dr. Connie Brett
▴ 10
0
votes
2
replies
95
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
47
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
updated 5 days ago by
James W. MacDonald
56k • written 5 days ago by
Laura
• 0
0
votes
1
reply
44
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 5 days ago by
Mike Smith
★ 4.9k • written 5 days ago by
Jeremy
• 0
2
votes
1
reply
41
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 5 days ago by
Kevin Blighe
2.8k • written 5 days ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
71
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
6 days ago • updated 1 day ago
xiaofeiwang18266
▴ 20
0
votes
0
replies
19
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
47
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 4 days ago by
Sam
▴ 10 • written 6 days ago by
ikumar2000
• 0
1
vote
15
replies
209
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
7 days ago • updated 4 days ago
demisa
• 0
1
vote
4
replies
88
views
EnhancedVolcano plot with colCustom
EnhancedVolcano
6 days ago • updated 1 day ago
Neeraja Vegesna
▴ 10
0
votes
2
replies
95
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
6 days ago
Kate
• 0
1
vote
1
reply
49
views
Enhanced Volcano Plot Controlling Color Layers
EnhancedVolcano
6 days ago
dk0319
• 0
4
votes
2
replies
77
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 6 days ago by
James W. MacDonald
56k • written 7 days ago by
Gero
• 0
40,586 results • Page
1 of 812
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Replies
Comment: How to filter all column using Loop
by
quincybatten
• 0
Iterating through pandas dataFrame objects is generally slow. Iteration beats the whole purpose of using DataFrame. It is an anti-pattern a…
Comment: clusterProfiler merge_result dotplot
by
jodi.thomas
• 0
Did you find a solution for this? I've also run into the exact same problem using merge_result on two gseaResult objects.
Answer: Pipeline for an Anova-like analysis in edgeR
by
Gordon Smyth
42k
The edgeR QL workflow illustrates a full pipeline: https://www.bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/i…
Comment: unable to forge custom BSgenome after update
by
Hervé Pagès
14k
From the updated vignette (unrendered): > If the assembly or genome has no circular sequence, set \code{circ\_seqs} to \code{character(0)}…
Comment: Sorting columns in pheatmap
by
Chris Seidel
▴ 70
If you set `cluster_cols=FALSE`, pheatmap will leave the order of the columns alone, and you can set it any way you like.
Votes
Answer: DESeq2 for TRAP-seq methods
A: p-values from robust linear model in LIMMA
Comment: unable to forge custom BSgenome after update
Comment: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
Answer: Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
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