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425
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News:
Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
11 months ago
info
▴ 10
0
votes
1
reply
451
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP
csaw
updated 11 months ago by
Aaron Lun
★ 29k • written 11 months ago by
Luca
• 0
0
votes
0
replies
303
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
11 months ago
User3088
• 0
0
votes
0
replies
315
views
News:
Announcing the GBCC2025 Logo Design Winner!
Community
Conference
GBCC2025
Bioconductor
11 months ago
Maria Doyle
▴ 110
0
votes
1
reply
480
views
building samplesheet and plot profile
DiffBind
11 months ago
yf
• 0
0
votes
0
replies
216
views
DBT JRF & PhD Scholar
BiologicalQuestion
OmicsMLRepoR
11 months ago
Manisha
• 0
0
votes
1
reply
445
views
I am having issues with bowtie2_build
genomes
bowtiew
Index
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
eduardo.pastor
• 0
0
votes
1
reply
698
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Sim
• 0
0
votes
0
replies
382
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
11 months ago
cftattersfield
• 0
1
vote
0
replies
646
views
News:
Bioconductor Course, Kenya 2025: Applications Open!
Events
Community
Training
Africa
Bioconductor
11 months ago
Maria Doyle
▴ 110
0
votes
2
replies
994
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
11 months ago • updated 10 months ago
ingrid.h
• 0
2
votes
2
replies
739
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
Nathan
• 0
9
votes
3
replies
2.6k
views
Job:
Postdoc/RA position: Software Engineer For R and High-Performance Computing
JobPosting
CuratedAtlasQueryR
tidySpatialExperiment
tidyomics
tidySingleCellExperiment
written 18 months ago by
Stefano Mangiola
▴ 40
0
votes
4
replies
1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
11 months ago
Quang NN
▴ 10
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 11 months ago by
franknappi14
• 0 • written 11 months ago by
Luca
• 0
4
votes
9
replies
3.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker
GenomeInfoDb
GenomicFeatures
Biostrings
gDNAx
updated 11 months ago by
Robert Castelo
★ 3.4k • written 12 months ago by
rohitsatyam102
▴ 20
0
votes
1
reply
649
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Reuben
• 0
0
votes
2
replies
605
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
11 months ago
Vinesh
• 0
0
votes
1
reply
372
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Harshul
• 0
0
votes
1
reply
402
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Anki
• 0
0
votes
2
replies
1.5k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
11 months ago
Blandine
• 0
0
votes
5
replies
786
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 11 months ago by
georgeyu703
• 0
0
votes
1
reply
482
views
affymetrix
genomes
Annotation
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
aurel.popa2011
• 0
0
votes
1
reply
2.2k
views
Problems with GSEA
GSEABase
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 11 months ago by
Sidra.Gull
• 0
0
votes
1
reply
550
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
11 months ago
ja.garcia
• 0
0
votes
4
replies
1.1k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
11 months ago
Quang NN
▴ 10
2
votes
4
replies
1.0k
views
EdgeR Biological CVs
edgeR
written 11 months ago by
James
• 0
0
votes
1
reply
541
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond
fish
updated 11 months ago by
Michael Love
43k • written 11 months ago by
brown.annaleigh
• 0
0
votes
0
replies
272
views
Problem with PCAtool as dependencie
COTAN
PCAtools
11 months ago
Silvia
• 0
1
vote
2
replies
485
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
written 13 months ago by
olusolaxx
• 0
0
votes
0
replies
327
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
11 months ago
xiaofeiwang18266
▴ 60
3
votes
5
replies
2.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Jonathan
▴ 10
0
votes
1
reply
426
views
XCMS Data Processing
r
xcms
metabolomi
NTA
Metabolomics
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
raklein
• 0
0
votes
2
replies
1.8k
views
Error using useMart or useEnsembl
biomaRt
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
rayanelkholdi
• 0
2
votes
1
reply
802
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
xiaofeiwang18266
▴ 60
0
votes
11
replies
1.5k
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 11 months ago by
Im
• 0 • written 11 months ago by
brown.annaleigh
• 0
0
votes
2
replies
1.0k
views
DESeq2 Heatmap
heatmaps
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
pm_25
• 0
0
votes
4
replies
2.1k
views
Biomart and ensembl not working?
ensembldb
biomaRt
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Zuzer
• 0
0
votes
1
reply
344
views
Unknown gene transcripts after annotatr
annotatr
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Zach
• 0
0
votes
1
reply
357
views
Improve performance of qusage aggregateGeneSet
qusage
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
oliverd
• 0
0
votes
0
replies
337
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
12 months ago • updated 11 months ago
nurkenber
• 0
0
votes
0
replies
403
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
12 months ago
GJ
• 0
0
votes
1
reply
432
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
linouhao
▴ 20
0
votes
0
replies
556
views
News:
Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
12 months ago
info
▴ 10
0
votes
2
replies
703
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 12 months ago by
svlachavas
▴ 840
0
votes
2
replies
913
views
iam not able to do retrive data using GEOquery R package
HELP
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
ramya20kumar20
• 0
2
votes
5
replies
907
views
Differential variability modelling with vst() expression
limma
DESeq2
written 12 months ago by
jtsy6383
• 0
0
votes
2
replies
542
views
Installation error for Rsamtools.
Rsamtools
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Sheila
• 0
3
votes
9
replies
2.2k
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi
EnsDb.Mmusculus.v79
biomaRt
org.Mm.eg.db
updated 11 months ago by
franknappi14
• 0 • written 12 months ago by
Nicholas
• 0
0
votes
3
replies
997
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 12 months ago by
sindhuri
• 0
46,710 results • Page
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Comment: Problem with the TMB plot
by
928380504
• 0
Itcapybara clicker is Slice Masternot o1v1 lolnlplanet clicker y level-devileasy to read bu Build Now GG|||| also make the conten more rich…
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[https://play-slice-master.com/][1][https://1v1-lol.cc/][2][https://planet-clicker.co/][3][https://play-level-devil.com/][4][https://buildn…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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