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9
views
Couldn't load org.Hs.eg.db
org.Hs.eg.db
1 hour ago
Chen
• 0
0
votes
1
reply
25
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 3 hours ago by
Michael Love
32k • written 15 hours ago by
Tom
• 0
0
votes
0
replies
16
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
3 hours ago • updated 2 hours ago
demisa
• 0
0
votes
3
replies
37
views
Problem with estimateSizeFactors due to avgTxLength
DESeq2
9 hours ago • updated 3 hours ago
Mark
• 0
20
votes
18
replies
588
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 2 hours ago by
Michelle
• 0 • written 2 days ago by
Arun
▴ 110
0
votes
0
replies
21
views
News:
Nominations for Bioconductor 2021 Awards!
Awards
Recognition
Bioconductor
Bioc2021
15 hours ago
shepherl
2.6k
0
votes
0
replies
20
views
News:
Bioconductor 3.13 New Package Submission Deadline
release
Submission
newpackage
Release
Deadline
17 hours ago
shepherl
2.6k
0
votes
0
replies
16
views
News:
Bioconductor Release 3.13 Schedule
Release
release
1 day ago • updated 17 hours ago
shepherl
2.6k
1
vote
1
reply
35
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 17 hours ago by
Michael Love
32k • written 1 day ago by
xiaofeiwang18266
▴ 20
0
votes
0
replies
25
views
Query regarding edgeR and limma
limma
readDGE
edgeR
17 hours ago
abhisekdey061
• 0
0
votes
2
replies
41
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta
BiocFileCache
updated 17 hours ago by
Michael Love
32k • written 1 day ago by
judith.risse
• 0
0
votes
0
replies
29
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl
minfi
1 day ago
jefflincoln4
• 0
3
votes
3
replies
57
views
DESeq2 two conditions with interaction
DESeq2
updated 9 hours ago by
Kevin Blighe
2.7k • written 1 day ago by
mboeck
• 0
0
votes
2
replies
234
views
News:
List of Deprecated Packages for Bioc3.13
Workflow
Software
Deprecation
ExperimentData
4 months ago • updated 1 day ago
shepherl
2.6k
0
votes
4
replies
67
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma
edgeR
rna
1 day ago
Nirad
• 0
0
votes
0
replies
17
views
News:
Bioc2021 Registration is Open
Conference
Bioc2021
1 day ago
shepherl
2.6k
0
votes
0
replies
17
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
1 day ago • updated 19 hours ago
Sam
▴ 10
0
votes
1
reply
48
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
updated 1 day ago by
Michael Love
32k • written 4 days ago by
Xianjun Dong
• 0
0
votes
3
replies
78
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
4 days ago • updated 1 day ago
jbono
• 0
4
votes
5
replies
88
views
edgeR for a mixture experiment
edgeR
model-selection
RRBS
mixture-experiment
1 day ago
ingerslev
• 0
1
vote
2
replies
70
views
BiomaRt conversion
biomaRt
25 days ago • updated 1 day ago
gwendal.lazennec
• 0
0
votes
0
replies
22
views
how to construct a SNPlocs-class by myself
BSgenome
SNPlocs
1 day ago
shangguandong1996
▴ 20
0
votes
2
replies
68
views
CRISPRseek package: 5’ PAM?
CRISPRseek
4 days ago • updated 1 day ago
nderian
• 0
3
votes
2
replies
59
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 2 days ago by
Gordon Smyth
42k • written 3 days ago by
Gero
• 0
0
votes
1
reply
46
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 2 days ago by
Guido Hooiveld
★ 2.9k • written 2 days ago by
Pierre-Alex
• 0
4
votes
4
replies
71
views
How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 1 day ago by
Laurent Gatto
1.5k • written 3 days ago by
rohitsatyam102
▴ 10
0
votes
0
replies
201
views
Job:
Bioinformatics Laboratory Head, WEHI, Melbourne, Australia
Australia
JobPosting
3 days ago
Gordon Smyth
42k
0
votes
2
replies
61
views
Limma experiment design and making contrasts
limma
methylationArrayAnalysis
3 days ago
Kesava
• 0
2
votes
2
replies
61
views
RSamtools idxstats does not return unmapped reads
Rsamtools
4 days ago • updated 3 days ago
mja18
▴ 40
1
vote
2
replies
66
views
RSamtools idxstatsBam not working with remote bam file
Rsamtools
4 days ago
mja18
▴ 40
0
votes
0
replies
33
views
Running > 100 samples per group - memory issues
xcms
memory
findchrompeaks
4 days ago
abrsoule
▴ 30
0
votes
0
replies
32
views
CAGEr consensusClustersDESeq2()
CAGEr
4 days ago
MatteoP
• 0
0
votes
0
replies
29
views
CAGEexp vs CAGErseq
CAGEr
4 days ago
MatteoP
• 0
0
votes
1
reply
36
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 4 days ago by
Johannes Rainer
★ 1.8k • written 4 days ago by
António Miguel de Jesus Domingues
▴ 480
0
votes
2
replies
62
views
Outliers
outliers
Deseq2
4 days ago
nolwenn
• 0
0
votes
0
replies
27
views
Gviz: set colors for UTRs
plot
color
Gviz
utr
4 days ago
ginlucks
• 0
0
votes
1
reply
38
views
Error in read.table function using multiclust
multiClust
updated 5 days ago by
Kevin Blighe
2.7k • written 5 days ago by
Debashis
• 0
0
votes
1
reply
41
views
log transformation the eset
codelink
updated 5 days ago by
Kevin Blighe
2.7k • written 5 days ago by
Yuxiii
• 0
3
votes
3
replies
122
views
Query regarding Differential gene expression analysis
limma
edgeR
DESeq2
6 days ago • updated 4 days ago
abhisekdey061
• 0
1
vote
4
replies
129
views
TCGA data analysis
RSEM
5 days ago • updated 4 days ago
lily
▴ 20
0
votes
11
replies
284
views
How to setup sample design in DESeq2
DESeq2
written 7 weeks ago by
dequattro.concetta
▴ 10
0
votes
0
replies
44
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
dispersion
DESeq2
polyester
5 days ago
catalina.gonzalez-gomez
• 0
2
votes
4
replies
79
views
BSGenome Forge for non-model organism
BSGenomeForge
BSGenome
updated 4 days ago by
Hervé Pagès
14k • written 6 days ago by
sieminsk
• 0
0
votes
3
replies
103
views
Issue loading data with tximeta
tximeta
updated 5 days ago by
Kevin Blighe
2.7k • written 7 days ago by
dshres
• 0
0
votes
6
replies
98
views
while doing co-expression network analysis, I am getting an error
RNASeqData
6 days ago • updated 5 days ago
Rishav
• 0
0
votes
1
reply
55
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest
minfi
conumee
updated 4 days ago by
Wang Yibo
• 0 • written 6 days ago by
theresa.walder
• 0
2
votes
4
replies
92
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
6 days ago • updated 5 days ago
sbcn
▴ 70
1
vote
12
replies
179
views
Data normalization
DESeq2
Normalization
6 days ago • updated 5 days ago
nolwenn
• 0
0
votes
1
reply
45
views
Deseq2 error "Error in designAndArgChecker"
DESeq2
updated 6 days ago by
Michael Love
32k • written 6 days ago by
polaxgr
▴ 10
2
votes
1
reply
69
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 6 days ago by
Rory Stark
★ 3.8k • written 8 days ago by
Sam
▴ 10
40,536 results • Page
1 of 811
Recent ...
Replies
Comment: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
by
Michelle
• 0
I am having the same issue, my code was working, I went to lunch and now it's not. The pathview, org.Mm.eg.db, and org.Hs.eg.db packages wo…
Answer: Using DESeq2 to identify changing transcriptional activity in a metagenome
by
Michael Love
32k
The design looks fine to me, similar to other posts on the support site of testing ratios (e.g. ribosomal profiling etc.). I would just not…
Comment: Problem with estimateSizeFactors due to avgTxLength
by
Michael Love
32k
By bringing up the size factors, I just wanted to point out that, this issue that scaled counts are not close to original counts happens wi…
Comment: Problem with estimateSizeFactors due to avgTxLength
by
Mark
• 0
Hi Michael, thank you for the response. I should probably clarify a couple of things and then request more clarification: - My library siz…
Answer: Problem with estimateSizeFactors due to avgTxLength
by
Michael Love
32k
hi Mark, Thanks for the post. I'd like to separate a few concepts, and then we can see how you consider each one. 1. Not trusting the es…
Votes
Comment: DESeq2 two conditions with interaction
Answer: Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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▴ 40
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