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0
votes
0
replies
100
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
16 days ago
daccar98
• 0
0
votes
0
replies
118
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
16 days ago
brayas13
• 0
2
votes
3
replies
658
views
featureCounts segmentation fault with large chromosomes
Rsubread
29 days ago • updated 17 days ago
vkkodali
▴ 10
0
votes
1
reply
353
views
Average expression of genes across replicates
DESeq2
updated 18 days ago by
ATpoint
★ 4.5k • written 19 days ago by
James
• 0
0
votes
1
reply
332
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 18 days ago by
ATpoint
★ 4.5k • written 19 days ago by
Katerina
• 0
0
votes
1
reply
421
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 19 days ago by
James W. MacDonald
67k • written 19 days ago by
mairahtkhan
• 0
0
votes
1
reply
412
views
Normalized counts to be used in decoupleR from deseq2 results
decoupleR
updated 19 days ago by
James W. MacDonald
67k • written 19 days ago by
James
• 0
2
votes
10
replies
1.5k
views
incomplete official symbol mitochondrial genes in org.Hs.eg.db?
org.Hs.eg.db
updated 8 days ago by
James W. MacDonald
67k • written 19 days ago by
Guido Hooiveld
★ 4.1k
0
votes
8
replies
390
views
Why are internal functions in the package manual?
roxygen
methyLImp2
manual
updated 19 days ago by
James W. MacDonald
67k • written 19 days ago by
anna
• 0
0
votes
0
replies
101
views
export processed data from flowploidy
flowPloidy
20 days ago
Zdenek Skala
• 0
0
votes
1
reply
212
views
edit y axis scale in errBarchart?
ddCt
updated 20 days ago by
James W. MacDonald
67k • written 21 days ago by
arustagi
• 0
2
votes
2
replies
659
views
Error: 'term_similarity_from_KEGG' not found in simplifyEnrichment package
simplifyEnrichment
updated 20 days ago by
James W. MacDonald
67k • written 21 days ago by
Yifeii.Ge
• 0
1
vote
0
replies
210
views
News:
Bioconductor 3.20 is Released!
Bioconductor
Release
Software
21 days ago
shepherl
4.1k
0
votes
0
replies
101
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
21 days ago
info
▴ 10
0
votes
1
reply
248
views
probe ID search for SNP (plink)
genomes
updated 21 days ago by
James W. MacDonald
67k • written 22 days ago by
유빈
• 0
2
votes
2
replies
370
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 21 days ago by
Guangchuang Yu
★ 1.2k • written 28 days ago by
Asma
• 0
0
votes
10
replies
1.2k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
22 days ago • updated 15 days ago
Denise
• 0
2
votes
2
replies
1.2k
views
Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
basilisk
updated 18 days ago by
ATpoint
★ 4.5k • written 22 days ago by
Stefano Mangiola
▴ 20
4
votes
6
replies
1.2k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus
biomaRt
updated 6 days ago by
Mike Smith
★ 6.6k • written 22 days ago by
Benjamin
▴ 20
0
votes
0
replies
67
views
Filtering Steps for proActiv Analysis
Transcriptomics
proActiv
22 days ago
LuciaNhu
• 0
2
votes
3
replies
581
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE
ReactomePA
22 days ago
Yifeii.Ge
• 0
0
votes
1
reply
308
views
Deseq to output continous sequencing data
DESeq2
updated 23 days ago by
Michael Love
42k • written 5 weeks ago by
Neha
• 0
1
vote
4
replies
732
views
Adjusted p-values become NA when sub-setting samples
DESeq2
5 weeks ago • updated 14 days ago
txema.heredia
• 0
3
votes
3
replies
825
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 25 days ago by
Satoshi
• 0
0
votes
0
replies
96
views
diffbind covariates
DiffBind
ATACSeq
updated 24 days ago by
Michael Love
42k • written 25 days ago by
Alpesh Querer
▴ 220
0
votes
0
replies
72
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
25 days ago
mario_de_manner
• 0
1
vote
4
replies
707
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 26 days ago by
Tyler Sagendorf
▴ 10 • written 6 weeks ago by
Bob
▴ 10
0
votes
3
replies
437
views
Its possible to remove annotation names using anno_simple in ComplexHeatmap
ComplexHeatmap
updated 26 days ago by
Tyler Sagendorf
▴ 10 • written 5 weeks ago by
nromerov
• 0
0
votes
4
replies
553
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs
edgeR
RNASeqData
26 days ago • updated 23 days ago
Philippine
• 0
1
vote
4
replies
595
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges
Biostrings
S4Vectors
written 26 days ago by
Christine Jones
• 0
2
votes
2
replies
385
views
Samples used for network inference in RegEnrich
RegEnrich
26 days ago
A.Barden
▴ 10
0
votes
0
replies
109
views
News:
Announcing the GBCC2025 Logo Design Contest!
Conference
Community
Galaxy
GBCC2025
Bioconductor
26 days ago
Maria Doyle
▴ 90
0
votes
3
replies
457
views
qvalue density function error
qvalue
26 days ago • updated 25 days ago
Tim
• 0
4
votes
3
replies
743
views
Analysis of 2*4 factorial design
limma
updated 21 days ago by
Gordon Smyth
51k • written 27 days ago by
Sudipta
• 0
2
votes
12
replies
1.4k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
updated 1 day ago by
Gordon Smyth
51k • written 26 days ago by
john
• 0
0
votes
2
replies
311
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 29 days ago by
Aleksandra
• 0
1
vote
3
replies
535
views
Tutorial regarding metabolomics with R
Bioconductor
Metabolomics
xcms
updated 28 days ago by
James W. MacDonald
67k • written 29 days ago by
abhisek001
• 0
1
vote
1
reply
379
views
DataFrame Character Truncation
S4Vectors
updated 28 days ago by
James W. MacDonald
67k • written 29 days ago by
Dario Strbenac
★ 1.5k
4
votes
6
replies
1.4k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 28 days ago by
Gordon Smyth
51k • written 29 days ago by
abadgerw
• 0
5
votes
13
replies
1.5k
views
Installing annotation package in locally
AnnotationDbi
AnnotationHub
Annotation
AnnotationForge
4 weeks ago • updated 28 days ago
KABILAN
• 0
0
votes
2
replies
419
views
DiffBind dba.report discrepancy
DiffBind
4 weeks ago • updated 28 days ago
aelbassiouny
• 0
1
vote
8
replies
962
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea
mice
org.Mm.eg.db
updated 28 days ago by
James W. MacDonald
67k • written 4 weeks ago by
Gordon
• 0
0
votes
1
reply
264
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
nicolettacommins
• 0
0
votes
2
replies
412
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
4 weeks ago • updated 28 days ago
José
• 0
0
votes
0
replies
74
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment
SingleCellExperiment
4 weeks ago
Ibrahim
• 0
0
votes
1
reply
174
views
MethylKit CpG Island annotation for Hg38
methylKit
updated 4 weeks ago by
James W. MacDonald
67k • written 4 weeks ago by
Satyanarayan
• 0
0
votes
5
replies
437
views
Need help converting vcf files to snp
VCFArray
4 weeks ago
patrice.bridges457
• 0
0
votes
0
replies
104
views
News:
List of Deprecated Packages for Bioc3.20
Devel
Bioconductor
Release
4 weeks ago • updated 27 days ago
shepherl
4.1k
0
votes
11
replies
1.6k
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 months ago • updated 4 weeks ago
shepherl
4.1k
4
votes
6
replies
1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
4 weeks ago • updated 24 days ago
altintas.ali
• 0
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Answer: Unlocking Potential: NURS FPX Strategies and Insights
by
efsane_kral2000
• 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights
by
efsane_kral2000
• 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
Comment: Is it recommended to analyze different tissues together when using edgeR
by
Gordon Smyth
51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data
by
Melisa Tecik
• 0
Thanks a lot for the help. You saved my day
Answer: Differene between the Wald and LRT test for time-series gene expression data
by
James W. MacDonald
67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
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Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Allele frequencies for ALL alleles of one SNP ?
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
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