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bioconductor.org not reachable from EU region
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1 hour ago
ashu.upadhyay2206
• 0
1
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5
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43
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The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2
RNASeq
3 hours ago • updated 1 hour ago
hequn
• 0
0
votes
1
reply
24
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DESeq2 coefficient names
resultsNames
DESeq2
coefficient
updated 2 hours ago by
Michael Love
32k • written 7 hours ago by
jkhudyakov
• 0
0
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1
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19
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Ensemble site connection error
biomaRt
updated 2 hours ago by
Kevin Blighe
2.8k • written 11 hours ago by
Makoto
• 0
0
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1
reply
24
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Deseq2 - removing batch effect
BatchEffect
DESeq2
updated 2 hours ago by
Kevin Blighe
2.8k • written 7 hours ago by
vinisha
• 0
0
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0
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9
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EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
3 hours ago
Marianna
• 0
1
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4
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1.2k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 12 hours ago by
Leonardo Collado Torres
▴ 870 • written 3.6 years ago by
maleknias
• 0
0
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1
reply
65
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News:
Bioconductor 3.13 New Package Submission Deadline
release
Submission
newpackage
Release
Deadline
9 days ago • updated 1 day ago
shepherl
2.6k
0
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0
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30
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DiffBind
ATACSeq
DiFFBind
1 day ago
Riba Michela
▴ 80
2
votes
3
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93
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Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
updated 15 hours ago by
Gordon Smyth
42k • written 1 day ago by
Antonio M.
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0
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2
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60
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GenomeInfoDb’ could not be loaded or installed
GenomeInfoDbData
updated 1 day ago by
Hervé Pagès
14k • written 2 days ago by
ettore64
• 0
0
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2
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138
views
Error: package or namespace load failed for ‘org.Hs.eg.db’:
$operator
atomicvectors
updated 1 day ago by
ramashan
• 0 • written 5 days ago by
dazhiruoyujingjie
• 0
1
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2
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62
views
DESeq2 for TRAP-seq methods
DESeq2
TRAP-seq
2 days ago • updated 1 day ago
marypiper
• 0
3
votes
3
replies
80
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DESeq2 unmix function
DESeq2
updated 2 hours ago by
Michael Love
32k • written 1 day ago by
Sam
▴ 10
1
vote
3
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86
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
2 days ago • updated 1 day ago
dantasezequiel1
• 0
0
votes
0
replies
21
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Job:
Bioinformatician / Software Developer with Flow Cytometry experience.
JobPosting
Flow-Cytometry
1 day ago
Martin
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1
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2
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50
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Sorting columns in pheatmap
pheatmap
2 days ago • updated 1 hour ago
Linda
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0
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6
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1.0k
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clusterProfiler: different runs return different results for gse functions
clusterprofiler
updated 2 days ago by
josep
• 0 • written 3.6 years ago by
ssv
• 0
0
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2
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53
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How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
2 days ago • updated 1 day ago
waiyin0923
• 0
3
votes
5
replies
90
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unable to forge custom BSgenome after update
BSgenome
updated 1 day ago by
Hervé Pagès
14k • written 2 days ago by
Chris Seidel
▴ 80
0
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0
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23
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Mass spec intensity difference
xcms
2 days ago
Phytochem
• 0
0
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0
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26
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Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
2 days ago
Thomas.H.Hampton
• 0
0
votes
1
reply
43
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Extract data from pair files
nimblegen
pair
updated 2 days ago by
James W. MacDonald
56k • written 3 days ago by
Dhanya
• 0
0
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0
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33
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News:
Support Site Bioconductor Award
recognition
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bioc2021
Bioconductor
2 days ago
shepherl
2.6k
2
votes
3
replies
82
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Which DESeq normalization method?
DESeq2
updated 2 days ago by
Michael Love
32k • written 3 days ago by
save
• 0
0
votes
2
replies
64
views
Error running ExperimentHubData::makeExperimentHubMetadata on Windows 10
BiocCheck
updated 2 days ago by
shepherl
2.6k • written 5 days ago by
wewolski
▴ 10
1
vote
2
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102
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Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
updated 3 days ago by
shepherl
2.6k • written 6 days ago by
Nicol
• 0
4
votes
4
replies
148
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
62
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
67
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3 days ago by
Michael Love
32k • written 4 days ago by
Pufall, Miles A
▴ 30
4
votes
2
replies
120
views
Error Loading "org.Dm.eg.db" package
r
org.Dm.eg.db
updated 3 days ago by
Chris Seidel
▴ 80 • written 3 days ago by
Amanda
▴ 20
3
votes
2
replies
65
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
4 days ago • updated 3 days ago
Assa Yeroslaviz
★ 1.5k
40
votes
29
replies
3.1k
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
36
views
PCA theoretical question for applied case
pcaMethods
4 days ago
Gero
• 0
2
votes
2
replies
284
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
5 days ago • updated 4 days ago
Jack
• 0
0
votes
0
replies
36
views
motifBreakR error with custom BSgenome
GenomeInfoDb
motifbreakR
5 days ago • updated 21 hours ago
Chris Seidel
▴ 80
1
vote
11
replies
250
views
Aspli: error with gbCounts
Aspli
ASpli
4 weeks ago • updated 1 day ago
jbono
▴ 10
1
vote
1
reply
55
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 6 days ago by
Michael Love
32k • written 6 days ago by
l.troxler
▴ 10
1
vote
8
replies
153
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 4 days ago by
Kevin Blighe
2.8k • written 7 days ago by
dorina.jamniczky
• 0
0
votes
9
replies
617
views
Thoughts on computer purchase
computer
updated 6 days ago by
Gordon Smyth
42k • written 15.0 years ago by
Lance Palmer
▴ 60
2
votes
2
replies
92
views
Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 3 days ago by
Kevin Blighe
2.8k • written 7 days ago by
Javier
• 0
0
votes
1
reply
33
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 6 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
157
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
65
views
Warning with the example of GSEA
fgsea
fgse
updated 6 days ago by
Kevin Blighe
2.8k • written 7 days ago by
julie.hardy
• 0
3
votes
2
replies
50
views
Biomart Errors
biomaRt
6 days ago
Dr. Connie Brett
▴ 10
0
votes
2
replies
97
views
DepMap copy number
software error
depmap
updated 4 days ago by
E
• 0 • written 6 months ago by
DannyM
• 0
0
votes
2
replies
62
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
7 days ago • updated 5 hours ago
Laura
• 0
0
votes
1
reply
46
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 6 days ago by
Mike Smith
★ 4.9k • written 7 days ago by
Jeremy
• 0
2
votes
1
reply
44
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 7 days ago by
Kevin Blighe
2.8k • written 7 days ago by
Assa Yeroslaviz
★ 1.5k
40,592 results • Page
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Replies
Comment: The correlation between normalized counts and TPM based on 2-factor analysis by
by
hequn
• 0
Thank you so much for you response. TPM is calculated by the company, I do not know which software they used to generate them. I had used…
Comment: Sorting columns in pheatmap
by
Linda
• 0
Thank you Chris that is really helpful. Now I have a situation whereby the columns are organised how I would like. However, it appears to…
Answer: The correlation between normalized counts and TPM based on 2-factor analysis by
by
Michael Love
32k
My first guess is that there is a bug in the merging code. I don't see anything in particular, but you've got a lot of code and whereas thi…
Comment: The correlation between normalized counts and TPM based on 2-factor analysis by
by
hequn
• 0
This is the code for figure 1 normalized_counts = as.data.frame(counts(dds, normalized = TRUE)) normalized_counts$ID = rownames(…
Comment: The correlation between normalized counts and TPM based on 2-factor analysis by
by
Michael Love
32k
Could you post your code where you make these plots?
Votes
Comment: Sorting columns in pheatmap
Comment: DESeq2 unmix function
Answer: DESeq2 unmix function
Comment: The correlation between normalized counts and TPM based on 2-factor analysis by
Answer: diffbind installation through Conda fails
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