3
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1
reply
2.3k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
0
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1
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591
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Risa package missing from Bioconductor 3.19
3.19 Risa
updated 18 months ago by 68k • written 18 months ago by • 0
1
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2
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1.2k
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Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
18 months ago ronin • 0
0
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0
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761
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
18 months ago JG13 • 0
0
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1
reply
793
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BiomaRt listAttributes - which are external ?
Bioconductor getBM
updated 18 months ago by 68k • written 18 months ago by • 0
0
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0
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848
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
18 months ago gamma.jian ▴ 10
1
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2
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3.4k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
18 months ago sropri • 0
0
votes
5
replies
1.1k
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 18 months ago by ▴ 760 • written 18 months ago by ▴ 760
1
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4
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2.5k
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SeSAMe DMR for EPIC V2
sesame EPICv2manifest epicv2
updated 5 months ago by • 0 • written 18 months ago by ▴ 50
1
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5
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2.2k
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EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
18 months ago Lluís Revilla Sancho ▴ 760
0
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5
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2.2k
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Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 18 months ago by 4.3k • written 19 months ago by • 0
4
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4
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1.8k
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Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
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18 months ago sukeshinik5 ▴ 20
0
votes
0
replies
494
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Structural Variant Format Converted for BRASS Format
StructuralVariantAnnotation
18 months ago Dario Strbenac ★ 1.6k
0
votes
1
reply
608
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 18 months ago by 68k • written 18 months ago by • 0
1
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2
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1.6k
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Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
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18 months ago Svitlana ▴ 10
0
votes
0
replies
499
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Differential Gene Wrapper for Propotion of Detected
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18 months ago Dario Strbenac ★ 1.6k
0
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2
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1.8k
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PCA (Principal Component Analysis) plots from ChIP-seq data
ChIPseqR
19 months ago • updated 18 months ago egbastakis • 0
4
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4
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1.2k
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Warning message when running limma with covariates
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18 months ago • updated 12 months ago Chris ▴ 20
0
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9
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1.5k
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
18 months ago gallantk5 • 0
3
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5
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3.6k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 18 months ago by • 0 • written 22 months ago by ▴ 60
0
votes
8
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2.3k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
19 months ago • updated 18 months ago jiachengd • 0
5
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5
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1.8k
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Limma with covariates
limma
written 19 months ago by ▴ 20
1
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1
reply
816
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
votes
2
replies
1.3k
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Epicv2 conversion fail
minfi
19 months ago • updated 18 months ago Alex • 0
1
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5
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1.2k
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DESeq2 ML Query
DESeq2
updated 18 months ago by 43k • written 19 months ago by • 0
1
vote
3
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1.1k
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
19 months ago • updated 17 months ago David W. H. • 0
0
votes
0
replies
854
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Job: Postdoc+PhD position: AI large-language models of single-cell data for cancer immunogenomics
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19 months ago Stefano Mangiola ▴ 40
0
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0
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1.0k
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19 months ago Stefano Mangiola ▴ 40
0
votes
0
replies
604
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Filtering the genesets for fgseaMultiLevel
msigdb fgsea msig
19 months ago Tanvi • 0
0
votes
1
reply
770
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1
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3
replies
2.0k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
19 months ago Tanvi • 0
2
votes
6
replies
1.6k
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Create multiple DoparParams with different number of registered cores
BiocParallel
updated 19 months ago by 68k • written 19 months ago by ★ 5.0k
1
vote
1
reply
848
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Otsu threshold segmentation using EBImage
EBImage
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
698
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News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
19 months ago shepherl 4.3k
2
votes
2
replies
1.7k
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biomaRt has encountered an unknown server error while using getLDS
BioMartGOGeneSets getLDS
19 months ago miriam.lloriansopena • 0
0
votes
2
replies
1.0k
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
19 months ago Mallory • 0
0
votes
0
replies
799
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Job: PhD-position in bioinformatics / computational biology
Epigenomics NGS Aging Biobase
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
0
replies
821
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ligand-receptor-interactions for bulk RNAseq in R
decoupleR
19 months ago silvaesilva.da • 0
0
votes
1
reply
1.4k
views
In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
2
votes
1
reply
703
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 10
0
votes
0
replies
662
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
19 months ago Reese • 0
2
votes
1
reply
873
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by ▴ 70
3
votes
13
replies
2.1k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 19 months ago by • 0 • written 19 months ago by • 0
0
votes
0
replies
507
views
Scoreplot for OPLS
splots
19 months ago devarti.mahakalkar • 0
1
vote
2
replies
1.3k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
19 months ago sawa • 0
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
4
votes
2
replies
2.2k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
19 months ago Rachael • 0
1
vote
9
replies
3.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 19 months ago by 68k • written 19 months ago by ▴ 10
0
votes
1
reply
944
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
529
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Error in drawHeatmap function
GeneOverlap heatmaps
19 months ago Johanna • 0
46,716 results • Page 21 of 935
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Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner • 0
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
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Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
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The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
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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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C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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