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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 17 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 17 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 20 days ago by
Yifeii.Ge
• 0
1
vote
0
replies
206
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 17 days ago by
ATpoint
★ 4.5k • written 21 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
580
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE
ReactomePA
22 days ago • updated 21 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
731
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
411
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
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efsane_kral2000
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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
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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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