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8
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
8 months ago
ktz
• 0
0
votes
0
replies
349
views
News:
Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq
MNaseSeq
ATACSeq
8 months ago
info
▴ 10
1
vote
2
replies
1.1k
views
Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
annotation
geneIDs
flatheadmullet
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
andremicc
• 0
0
votes
1
reply
866
views
News:
List of Deprecated Packages for Bioc3.20
Release
Devel
Bioconductor
13 months ago • updated 8 months ago
shepherl
4.2k
0
votes
0
replies
18
views
Spam:
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org.Sc.sgd.db
8 months ago
irenejoshi07
0
1
vote
2
replies
1.4k
views
Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors
generic_find_knn
scran
quickCluster
8 months ago
Arctic
• 0
0
votes
1
reply
772
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
Cosmic
• 0
0
votes
1
reply
720
views
Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis
MethylationArrayData
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
luisa.turco
• 0
4
votes
6
replies
1.6k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 8 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Elijah
• 0
0
votes
4
replies
1.5k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
8 months ago
Sofia
• 0
1
vote
1
reply
1.0k
views
ComBat with repeated measures
ComBat
sva
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
s20
• 0
0
votes
0
replies
440
views
News:
List of Deprecated Packages for Bioc3.21
devel
Release
release
Devel
8 months ago
shepherl
4.2k
0
votes
0
replies
565
views
News:
Bioconductor 3.21 Release Schedule Important Deadlines Approaching
Software
Release
release
8 months ago
shepherl
4.2k
0
votes
0
replies
246
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
8 months ago
user_bioinfo
• 0
0
votes
0
replies
4
views
Spam:
Does Spirit give free refunds?
ncdfFlow
hcg110.db
MethylSeekR
8 months 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
8 months ago
Haggu
10
1
vote
0
replies
22
views
Spam:
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cadd.v1.6.hg38
MafDb.1Kgenomes.phase1.GRCh38
ncdfFlow
8 months 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
8 months ago
Haggu
10
0
votes
0
replies
8
views
Spam:
vjkftykdtyk
proDA
hcg110.db
zlibbioc
8 months ago
Haggu
10
2
votes
2
replies
1.5k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
robinpaul85
• 0
0
votes
3
replies
1.0k
views
Merging EPICV1 and V2 betas
minfiDataEPIC
minfi
updated 6 months ago by
Henry
• 0 • written 8 months ago by
rania.alanany
• 0
0
votes
1
reply
623
views
Error in cnetplot
enrichplot
clusterProfiler
updated 8 months ago by
Guido Hooiveld
★ 4.1k • written 8 months ago by
Ayesha
• 0
0
votes
3
replies
856
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf
biomaRt
Ensembl
updated 8 months ago by
Mike Smith
★ 6.6k • written 8 months ago by
Benjamin
▴ 20
2
votes
4
replies
997
views
Explanation for ROAST results
CAMERA
limma
written 8 months ago by
Jiahao Tian
• 0
1
vote
1
reply
437
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
AL
• 0
0
votes
2
replies
648
views
Annotation package for Manduca sexta
annotation
Manducasexta
AnnotationData
8 months ago
GA
▴ 10
0
votes
5
replies
887
views
Bioconductor unable to update 'curl'
curl
HELP
8 months ago
kagodwi2
• 0
0
votes
4
replies
2.4k
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 7 months ago by
darylruiz6545
• 0 • written 8 months ago by
hebda
• 0
0
votes
1
reply
366
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Alexander
• 0
1
vote
2
replies
1.4k
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2
EPICv2manifest
8 months ago
Joshua Llano
• 0
1
vote
4
replies
761
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
8 months ago
Lennie
• 0
4
votes
5
replies
1.7k
views
Using TPM from tximport of Salmon output for singscore
singscore
9 months ago • updated 8 months ago
Kent
• 0
5
votes
3
replies
1.2k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 8 months ago by
Gordon Smyth
53k • written 8 months ago by
Devin
▴ 10
2
votes
10
replies
4.5k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 9 months ago by
Josh
• 0 • written 2.6 years ago by
angel
• 0
0
votes
1
reply
494
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
9 months ago • updated 8 months ago
Lucas
• 0
0
votes
2
replies
432
views
myvariant error
myvariant
getVariants
updated 9 months ago by
Christelle
• 0 • written 9 months ago by
Christelle
• 0
0
votes
4
replies
1.2k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 9 months ago by
questionanswer
• 0
0
votes
0
replies
259
views
DiffBind multi-tissue comparison
DiffBind
9 months ago
lryrainche
• 0
1
vote
2
replies
674
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
akp9132
• 0
0
votes
0
replies
475
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
9 months ago
GT
• 0
1
vote
2
replies
1.2k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
9 months ago • updated 6 months ago
Erika
• 0
0
votes
2
replies
857
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
9 months ago • updated 8 months ago
DavideSant
• 0
2
votes
2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
9 months ago
Elizabeth
• 0
1
vote
8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 months ago • updated 8 months ago
Luca
• 0
0
votes
1
reply
482
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
flowreen.shikwana
• 0
1
vote
3
replies
1.2k
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
written 9 months ago by
AB
▴ 110
0
votes
1
reply
439
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
ramya2kumar0
• 0
0
votes
4
replies
879
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
9 months ago
Nicholas
• 0
0
votes
1
reply
564
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools
BiomedicalInformatics
GeneExpression
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Kiana
• 0
0
votes
0
replies
294
views
Simple confidence intervall Gviz
Gviz
9 months ago
William
• 0
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Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
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Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
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4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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