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compute_fasta_digest does not match Salmon index hash
tximeta
9 days ago • updated 6 hours ago
Alex
• 0
0
votes
0
replies
21
views
News:
Epigenomics data analysis with R and Bioconductor
chipseq
MNaseSeq
ATACSeq
1 day ago
info
▴ 10
1
vote
2
replies
330
views
Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
annotation
geneIDs
flatheadmullet
updated 1 day ago by
James W. MacDonald
68k • written 1 day ago by
andremicc
• 0
0
votes
1
reply
399
views
News:
List of Deprecated Packages for Bioc3.20
Release
Devel
Bioconductor
5 months ago • updated 1 day ago
shepherl
4.1k
0
votes
1
reply
85
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 1 day ago by
dirty.cougar.risi
• 0 • written 1 day ago by
Μαρία
• 0
0
votes
0
replies
18
views
Spam:
Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
3 days ago
irenejoshi07
0
1
vote
2
replies
1.1k
views
Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors
generic_find_knn
scran
quickCluster
5 days ago • updated 4 days ago
Arctic
• 0
0
votes
1
reply
498
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 5 days ago by
ATpoint
★ 4.8k • written 6 days ago by
Cosmic
• 0
0
votes
1
reply
488
views
Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis
MethylationArrayData
updated 6 days ago by
James W. MacDonald
68k • written 6 days ago by
luisa.turco
• 0
1
vote
4
replies
1.3k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
7 days ago • updated 6 days ago
slizchap
• 0
4
votes
6
replies
1.1k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 6 days ago by
ATpoint
★ 4.8k • written 29 days ago by
Elijah
• 0
0
votes
4
replies
1.1k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
7 days ago • updated 2 days ago
Sofia
• 0
1
vote
1
reply
721
views
ComBat with repeated measures
ComBat
sva
updated 6 days ago by
ATpoint
★ 4.8k • written 7 days ago by
s20
• 0
0
votes
0
replies
40
views
News:
List of Deprecated Packages for Bioc3.21
devel
Release
release
Devel
7 days ago
shepherl
4.1k
0
votes
0
replies
45
views
News:
Bioconductor 3.21 Release Schedule Important Deadlines Approaching
Software
Release
release
7 days ago
shepherl
4.1k
0
votes
0
replies
50
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
8 days ago
user_bioinfo
• 0
0
votes
0
replies
4
views
Spam:
Does Spirit give free refunds?
ncdfFlow
hcg110.db
MethylSeekR
9 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
9 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
9 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
9 days ago
Haggu
10
0
votes
0
replies
8
views
Spam:
vjkftykdtyk
proDA
hcg110.db
zlibbioc
9 days ago
Haggu
10
0
votes
2
replies
629
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 8 days ago by
ATpoint
★ 4.8k • written 9 days ago by
robinpaul85
• 0
0
votes
2
replies
387
views
Merging EPICV1 and V2 betas
minfiDataEPIC
minfi
updated 7 days ago by
Garbayo
• 0 • written 9 days ago by
rania.alanany
• 0
0
votes
1
reply
170
views
Error in cnetplot
enrichplot
clusterProfiler
updated 9 days ago by
Guido Hooiveld
★ 4.1k • written 15 days ago by
Ayesha
• 0
0
votes
3
replies
487
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf
biomaRt
Ensembl
updated 8 days ago by
Mike Smith
★ 6.6k • written 9 days ago by
Benjamin
▴ 20
2
votes
3
replies
640
views
Explanation for ROAST results
CAMERA
limma
updated 8 days ago by
Gordon Smyth
52k • written 9 days ago by
Jay
• 0
0
votes
0
replies
160
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
9 days ago
Simran
• 0
1
vote
1
reply
144
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 9 days ago by
James W. MacDonald
68k • written 10 days ago by
AL
• 0
0
votes
2
replies
356
views
Annotation package for Manduca sexta
annotation
Manducasexta
AnnotationData
10 days ago • updated 8 days ago
GA
▴ 10
0
votes
5
replies
269
views
Bioconductor unable to update 'curl'
curl
HELP
10 days ago
kagodwi2
• 0
0
votes
4
replies
364
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 9 days ago by
mdeea123
▴ 10 • written 10 days ago by
hebda
• 0
0
votes
1
reply
147
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 10 days ago by
James W. MacDonald
68k • written 13 days ago by
Alexander
• 0
1
vote
2
replies
1.1k
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2
EPICv2manifest
14 days ago • updated 7 days ago
Joshua Llano
• 0
1
vote
4
replies
368
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
14 days ago • updated 9 days ago
Lennie
• 0
4
votes
5
replies
1.3k
views
Using TPM from tximport of Salmon output for singscore
singscore
16 days ago • updated 13 days ago
Kent
• 0
5
votes
3
replies
770
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 15 days ago by
Gordon Smyth
52k • written 16 days ago by
Devin
▴ 10
2
votes
10
replies
3.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 16 days ago by
Josh
• 0 • written 23 months ago by
angel
• 0
0
votes
1
reply
187
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
16 days ago • updated 14 days ago
Lucas
• 0
0
votes
2
replies
251
views
myvariant error
myvariant
getVariants
updated 16 days ago by
Christelle
• 0 • written 4 weeks ago by
Christelle
• 0
0
votes
4
replies
467
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 17 days ago by
questionanswer
• 0
0
votes
0
replies
39
views
DiffBind multi-tissue comparison
DiffBind
17 days ago
lryrainche
• 0
1
vote
2
replies
392
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
updated 17 days ago by
James W. MacDonald
68k • written 19 days ago by
akp9132
• 0
0
votes
4
replies
269
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
17 days ago • updated 16 days ago
Wolfgang RAFFELSBERGER
▴ 140
0
votes
0
replies
114
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
18 days ago
GT
• 0
1
vote
1
reply
771
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 20 days ago by
James W. MacDonald
68k • written 20 days ago by
Erika
• 0
0
votes
2
replies
614
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
21 days ago • updated 15 days ago
DavideSant
• 0
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
23 days ago • updated 17 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
23 days ago • updated 22 days ago
Luca
• 0
0
votes
1
reply
283
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 22 days ago by
James W. MacDonald
68k • written 23 days ago by
flowreen.shikwana
• 0
1
vote
3
replies
830
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
written 24 days ago by
AB
▴ 110
46,431 results • Page
1 of 929
Recent ...
Replies
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Comment: Question on displaying color photo as Greyscale in EBImage
by
Albert
• 0
great and very nice
Comment: European Bioconductor Conference 2023 planning
by
Pandora
• 0
The [Tag Game][1] is not just a simple chase; it involves strategy and tactics as players must think quickly to avoid being tagged. Various…
Comment: Generalized edgeR functions
by
bukarimanches
• 0
I have estimated the new parameter set, it doesn't seem as useful as I thought [geometry dash lite][1] [1]: https://geometry-lite.com/
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
Morse
• 0
[Geometry Dash Lite][1] is the free version of the famous Geometry Dash series. It was made by RobTop Games and lets players enjoy the thri…
Votes
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
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