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DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 3 hours ago by
ATpoint
★ 4.8k • written 16 hours ago by
Cosmic
• 0
0
votes
1
reply
395
views
Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis
MethylationArrayData
updated 1 day ago by
James W. MacDonald
68k • written 1 day ago by
luisa.turco
• 0
1
vote
4
replies
676
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
2 days ago • updated 22 hours ago
slizchap
• 0
4
votes
6
replies
1.1k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 1 day ago by
ATpoint
★ 4.8k • written 23 days ago by
Elijah
• 0
0
votes
2
replies
401
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
updated 1 day ago by
Mike Smith
★ 6.6k • written 2 days ago by
Sofia
• 0
1
vote
1
reply
298
views
ComBat with repeated measures
ComBat
sva
updated 1 day ago by
ATpoint
★ 4.8k • written 2 days ago by
s20
• 0
0
votes
0
replies
25
views
News:
List of Deprecated Packages for Bioc3.21
devel
Release
release
Devel
2 days ago
shepherl
4.1k
0
votes
0
replies
23
views
News:
Bioconductor 3.21 Release Schedule Important Deadlines Approaching
Software
Release
release
2 days ago
shepherl
4.1k
0
votes
0
replies
38
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
3 days ago
user_bioinfo
• 0
0
votes
0
replies
3
views
Spam:
Does Spirit give free refunds?
ncdfFlow
hcg110.db
MethylSeekR
3 days ago
Haggu
10
0
votes
0
replies
28
views
Spam:
Can I change my BA flight to another date?
org.Sc.sgd.db
MafDb.1Kgenomes.phase1.GRCh38
ncdfFlow
3 days ago
Haggu
10
1
vote
0
replies
22
views
Spam:
What is the cheapest day to fly on American Airlines? {Ask_Expert}
cadd.v1.6.hg38
MafDb.1Kgenomes.phase1.GRCh38
ncdfFlow
3 days ago
Haggu
10
0
votes
0
replies
41
views
Spam:
Can I cancel my British Airways flight and get a refund?
CAGEr
gep2pep
hcg110.db
3 days ago
Haggu
10
0
votes
0
replies
8
views
Spam:
vjkftykdtyk
proDA
hcg110.db
zlibbioc
3 days ago
Haggu
10
0
votes
2
replies
608
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 3 days ago by
ATpoint
★ 4.8k • written 3 days ago by
robinpaul85
• 0
0
votes
2
replies
368
views
Merging EPICV1 and V2 betas
minfiDataEPIC
minfi
updated 1 day ago by
Garbayo
• 0 • written 3 days ago by
rania.alanany
• 0
0
votes
0
replies
30
views
compute_fasta_digest does not match Salmon index hash
tximeta
3 days ago
Alex
• 0
0
votes
1
reply
148
views
Error in cnetplot
enrichplot
clusterProfiler
updated 4 days ago by
Guido Hooiveld
★ 4.1k • written 10 days ago by
Ayesha
• 0
0
votes
3
replies
463
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf
biomaRt
Ensembl
updated 3 days ago by
Mike Smith
★ 6.6k • written 4 days ago by
Benjamin
▴ 20
2
votes
3
replies
616
views
Explanation for ROAST results
CAMERA
limma
updated 3 days ago by
Gordon Smyth
52k • written 4 days ago by
Jay
• 0
0
votes
0
replies
67
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
4 days ago
Simran
• 0
1
vote
1
reply
122
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 4 days ago by
James W. MacDonald
68k • written 4 days ago by
AL
• 0
0
votes
2
replies
329
views
Annotation package for Manduca sexta
annotation
Manducasexta
AnnotationData
4 days ago • updated 2 days ago
GA
▴ 10
0
votes
5
replies
241
views
Bioconductor unable to update 'curl'
curl
HELP
5 days ago
kagodwi2
• 0
0
votes
4
replies
293
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 4 days ago by
mdeea123
▴ 10 • written 5 days ago by
hebda
• 0
0
votes
1
reply
113
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 5 days ago by
James W. MacDonald
68k • written 7 days ago by
Alexander
• 0
1
vote
2
replies
985
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2
EPICv2manifest
9 days ago • updated 2 days ago
Joshua Llano
• 0
1
vote
4
replies
357
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
9 days ago • updated 4 days ago
Lennie
• 0
4
votes
5
replies
1.3k
views
Using TPM from tximport of Salmon output for singscore
singscore
11 days ago • updated 8 days ago
Kent
• 0
5
votes
3
replies
757
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 9 days ago by
Gordon Smyth
52k • written 10 days ago by
Devin
▴ 10
2
votes
10
replies
3.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 11 days ago by
Josh
• 0 • written 23 months ago by
angel
• 0
0
votes
1
reply
179
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
11 days ago • updated 8 days ago
Lucas
• 0
0
votes
2
replies
239
views
myvariant error
myvariant
getVariants
updated 11 days ago by
Christelle
• 0 • written 26 days ago by
Christelle
• 0
0
votes
4
replies
440
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 11 days ago by
questionanswer
• 0
0
votes
0
replies
34
views
DiffBind multi-tissue comparison
DiffBind
11 days ago
lryrainche
• 0
1
vote
2
replies
384
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
updated 12 days ago by
James W. MacDonald
68k • written 13 days ago by
akp9132
• 0
0
votes
4
replies
250
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
12 days ago • updated 11 days ago
Wolfgang RAFFELSBERGER
▴ 140
0
votes
0
replies
89
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
12 days ago
GT
• 0
1
vote
1
reply
765
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 14 days ago by
James W. MacDonald
68k • written 15 days ago by
Erika
• 0
0
votes
2
replies
602
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
16 days ago • updated 10 days ago
DavideSant
• 0
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
18 days ago • updated 12 days ago
Elizabeth
• 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
17 days ago • updated 16 days ago
Luca
• 0
0
votes
1
reply
276
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 17 days ago by
James W. MacDonald
68k • written 17 days ago by
flowreen.shikwana
• 0
1
vote
3
replies
810
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
written 18 days ago by
AB
▴ 110
0
votes
1
reply
173
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 18 days ago by
shepherl
4.1k • written 18 days ago by
ramya2kumar0
• 0
0
votes
4
replies
512
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
22 days ago • updated 12 days ago
Nicholas
• 0
0
votes
1
reply
281
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools
BiomedicalInformatics
GeneExpression
updated 19 days ago by
James W. MacDonald
68k • written 19 days ago by
Kiana
• 0
0
votes
0
replies
54
views
Simple confidence intervall Gviz
Gviz
19 days ago
William
• 0
1
vote
3
replies
19k
views
Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by
Mengfei
• 0
0
votes
2
replies
373
views
org.Hs.eg.db issue
org.Hs.eg.db
written 11 weeks ago by
k.panov
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Answer: DESeq2
by
ATpoint
★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer, very useful!
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Mike Smith
★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Answer: Mismatch between Illumina Mouse Methylation BeadChip annotation and genome brows
by
James W. MacDonald
68k
The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
Votes
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
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