1
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1
reply
2.0k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 11 months ago by 43k • written 5.3 years ago by • 0
4
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3
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656
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plyranges: find exact GRanges match keeping metadata columns
plyranges
updated 11 months ago by 43k • written 11 months ago by • 0
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0
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426
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News: Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
11 months ago info ▴ 10
0
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1
reply
454
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 11 months ago by ★ 29k • written 11 months ago by • 0
0
votes
0
replies
304
views
Batch Correction while implementing QSEA package
qsea MEDIPS MEDIPSData DNAMethylation
11 months ago User3088 • 0
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0
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316
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11 months ago Maria Doyle ▴ 110
0
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1
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483
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building samplesheet and plot profile
DiffBind
11 months ago yf • 0
0
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0
replies
218
views
DBT JRF & PhD Scholar
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11 months ago Manisha • 0
0
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1
reply
446
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I am having issues with bowtie2_build
genomes bowtiew Index
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
698
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
383
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
652
views
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11 months ago Maria Doyle ▴ 110
0
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2
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1.0k
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
11 months ago ingrid.h • 0
2
votes
2
replies
740
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
9
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3
replies
2.6k
views
Job: Postdoc/RA position: Software Engineer For R and High-Performance Computing
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written 19 months ago by ▴ 40
0
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4
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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 • 0 • written 11 months ago by • 0
4
votes
9
replies
3.1k
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Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 11 months ago by ★ 3.4k • written 12 months ago by ▴ 20
0
votes
1
reply
656
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
2
replies
616
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
11 months ago Vinesh • 0
0
votes
1
reply
374
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
1
reply
403
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 11 months ago by 68k • written 11 months ago by • 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
791
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 • 0
0
votes
1
reply
485
views
affymetrix
genomes Annotation
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
2.2k
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Problems with GSEA
GSEABase
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
1
reply
551
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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 • 0
0
votes
1
reply
544
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 43k • written 11 months ago by • 0
0
votes
0
replies
273
views
Problem with PCAtool as dependencie
COTAN PCAtools
11 months ago Silvia • 0
1
vote
2
replies
490
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
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written 13 months ago by • 0
0
votes
0
replies
330
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 68k • written 11 months ago by ▴ 10
0
votes
1
reply
432
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 11 months ago by 68k • written 12 months ago by • 0
0
votes
2
replies
1.8k
views
Error using useMart or useEnsembl
biomaRt
updated 11 months ago by 68k • written 11 months ago by • 0
2
votes
1
reply
804
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Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 11 months ago by 68k • written 11 months ago by ▴ 60
0
votes
11
replies
1.6k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 11 months ago by • 0 • written 12 months ago by • 0
0
votes
2
replies
1.0k
views
DESeq2 Heatmap
heatmaps
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
votes
4
replies
2.1k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
349
views
Unknown gene transcripts after annotatr
annotatr
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
359
views
Improve performance of qusage aggregateGeneSet
qusage
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
0
replies
339
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
12 months ago nurkenber • 0
0
votes
0
replies
405
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 68k • written 12 months ago by ▴ 20
0
votes
0
replies
559
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
12 months ago info ▴ 10
0
votes
2
replies
704
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 ▴ 840
0
votes
2
replies
924
views
iam not able to do retrive data using GEOquery R package
HELP
updated 12 months ago by 68k • written 12 months ago by • 0
2
votes
5
replies
913
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 0
0
votes
2
replies
546
views
Installation error for Rsamtools.
Rsamtools
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
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Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
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Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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