This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
1 reply
106 views
clusterProfiler GSEA (gseGO/gseKEGG): full ranked list vs DEG list, BH correction, and GO collapsing under FDR
go kegg gsea clusterprofiler
updated by Arup Ghosh Arup Ghosh • written by ki • ki
1 vote
0 replies
59 views
News: Pavel Pevzner to give an invited talk at CIBB 2026 (Rome, Sept 2-4)
bioinformatics biostatistics ai machine-learning
written by Umberto • Umberto
0 votes
0 replies
50 views
Tool: BioArena: blind comparison arena for AI models on biomedical questions
benchmarking bioinformatics ai llm tool
written by Rong • Rong
0 votes
1 reply
76 views
Troubleshooting an MLPA-confirmed OPA1 exon duplication missing in ONT Long-Read SV callers (cuteSV/Sniffles)
cnv nanopore structural-variation variant-calling mlpa
updated by colindaven colindaven • written by Kevin • Kevin
0 votes
3 replies
182 views
WGS-based SNP phylogeny - how to include accessions from an outgroup species
outgroup snp vcf phylogeny wgs
updated by colindaven colindaven • written by maxrwjones • maxrwjones
0 votes
4 replies
1.7K views
Python deconvolution tools for bulk RNA-seq data
rna-seq bulk-rna-seq deconvolution python transcriptomics
updated by Bernhard • Bernhard • written by AlexStar • AlexStar
0 votes
12 replies
522 views
R1 / R2 are out of sync
pair proper
written by Jon • Jon
0 votes
0 replies
45 views
News: Workshop: Virtual ChIP-Seq / ATAC-Seq – July 28–30, 2026
virtual chipseq workshop atacseq uconn
written by zsc25001 • zsc25001
0 votes
0 replies
53 views
News: Advanced Python for Data Science and Bioinformatics
machinelarning datascience python dataanalysis
written by Physalia-courses Physalia-courses
0 votes
0 replies
80 views
Job: Postdoctoral Fellow in Single-Nucleus Studies of Psychiatric and Substance Use Disorders
bioinformatics
written by ejvandenoord • ejvandenoord
0 votes
2 replies
138 views
News: Webinar: Are your NGS workflows ready for GMP?
gxp gmp ngs
updated by Michael Dondrup Michael Dondrup • written by Nicole • Nicole
0 votes
3 replies
210 views
Forum: Has online bioinformatics training replaced in-person courses?
in-person bioinformatics workshop online training
updated by Michael Dondrup Michael Dondrup • written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
0 replies
57 views
News: Deep Learning for Evolutionary Genomics
evolutionarygenomics deeplearning
updated by GenoMax GenoMax • written by coursesinfo • coursesinfo
0 votes
0 replies
49 views
News: Population Genomics and Structure Analysis
population genomics
updated by GenoMax GenoMax • written by coursesinfo • coursesinfo
0 votes
0 replies
36 views
Tool: Biomedical Evidence Navigator: a free tool to pull a single gene/variant/disease evidence report from PubMed, GWAS Catalog, ClinVar & Open Targets
agent python biomedical tool
written by Tunahan • Tunahan
0 votes
0 replies
43 views
News: Webinar: Programming Biology with Genome-scale AI - 10 August - 3 PM CEST
genomics ai programming
updated by GenoMax GenoMax • written by Physalia-courses Physalia-courses
0 votes
1 reply
113 views
single cell
redisplay
updated by ATpoint ATpoint • written by Victor • Victor
0 votes
3 replies
188 views
Why does MEGAHIT --min-contig-len 1 produce fewer long contigs than --min-contig-len 500 in a two-pass metagenomic assembly?
megahit metagenomics
updated by Ram Ram • written by Sachin • Sachin
0 votes
5 replies
228 views
Tool: HuskHoard – POSIX-transparent lazy loading for large Parquet/S3 datasets
storage
updated by GenoMax GenoMax • written by jo • jo
0 votes
4 replies
218 views
Best practices and parameter optimization for aligning highly degraded ancient S. mutans genomes?
bwa alignment variant-calling metagenomics ancient-dna
written by oguzhanisilay • oguzhanisilay
0 votes
2 replies
117 views
SnpEff build fails with custom Saccharomyces cerevisiae database (R64-4-1) - Protein check "Not found" vs "OK" split
custom_database snpeff s.cerevisiae
updated by GenoMax GenoMax • written by mohammaddaud046 • mohammaddaud046
2 votes
2 replies
1.6K views
pvalueCutoff for enrichGO, enrichKEGG and enrichDO does not seem to function properly
clusterprofiler
updated by Guillermo • Guillermo • written by t.mcgovern • t.mcgovern
9 votes
0 replies
176 views
Blog: Fable is not a useful model
anthropic ai safety
updated by LauferVA LauferVA • written by Rob Rob
0 votes
0 replies
54 views
News: Landscape Genomics course
populationgenomics landscapegenomics r
written by Physalia-courses Physalia-courses
0 votes
0 replies
49 views
News: Instructor-led online training - Population Genomics and Structure Analysis
population genomics
updated by GenoMax GenoMax • written by coursesinfo • coursesinfo
0 votes
0 replies
65 views
Tool: Update: Jetomics v2.0 – Now with Local FASTQ Pipelines, Xenium Spatial Support, and Free Academic Licensing
rna-seq xenium spatial transcriptomics
written by Aram Donyaee • Aram Donyaee
0 votes
5 replies
315 views
single cell processed data
single-cell
updated by marco.barr • marco.barr • written by Aya • Aya
0 votes
8 replies
18K views
How to load data into R from an external hard drive?
r load rstudio unix
updated by Dexter Watts • Dexter Watts • written by M.O.L.S • M.O.L.S
0 votes
1 reply
116 views
I need help clustering genes across different timepoints AND multiple tissues
advice help clustering
updated by manaswwm manaswwm • written by mohammad.naweed • mohammad.naweed
0 votes
0 replies
51 views
Looking for messy GFF3 examples to test a Rust AGAT-compatible gxf2gxf beta
gtf agat genome-annotation gff3
updated by Ram Ram • written by Ben • Ben
0 votes
3 replies
169 views
How can I visualize the Gene Ontology hierarchy for a set of GO terms in R?
ontology go plotting r
updated by Arup Ghosh Arup Ghosh • written by fnepo • fnepo
10 votes
18 replies
12K views
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers conference
updated by James Michael Smith • James Michael Smith • written by Brandstaetter Brandstaetter
0 votes
0 replies
63 views
Tool: Free IgGM Server
iggm antibody design
written by immunology_bishop • immunology_bishop
2 votes
12 replies
22K views
How to transpose large amounts of datasets in excel
transpose excel
updated by Ram Ram • written by Vanceed • Vanceed
0 votes
0 replies
86 views
News: Why does every R tutorial work... Except on my own data?
tidyverse messydata r
written by Physalia-courses Physalia-courses
0 votes
0 replies
65 views
Tool: Free browser tool: HPO interactive graph , clinical note to HPO terms (client-side, no PHI upload)
phenotype hpo clinical-nlp
updated by GenoMax GenoMax • written by mchandrahasreddy • mchandrahasreddy
1 vote
4 replies
238 views
Ranking Seurat markers for annotation — are pct.1/pct.2 standard, or is log2FC + adjusted p-value enough
snrna sequencing clustering annotation
updated by GenoMax GenoMax • written by Arindam • Arindam
0 votes
3 replies
226 views
News: Free AI/ML for Genomics course with Colab notebooks, Geneformer, scVI, AlphaGenome
machine deep learning transformers
written by aadil • aadil
0 votes
8 replies
4.7K views
How to compute enrichment of one feature in the other across the genome (log fold, and pvalue)
genome enrichment
updated by eebloom • eebloom • written by User 7754 User 7754
0 votes
0 replies
52 views
News: (Workshop) RNAseq data analysis with R and Bioconductor
genesetenrichmentanalysis bioconductor rnaseq r
written by Physalia-courses Physalia-courses
0 votes
0 replies
52 views
Tool: ctdR: enrichment analysis of chemical–gene interactions from the Comparative Toxicogenomics Database
ctd bioconductor enrichment r toxicogenomics
written by l.corsaro • l.corsaro
0 votes
2 replies
137 views
Evigene and ORF prediction
start orf codon evigene
updated by GenoMax GenoMax • written by Lucija • Lucija
0 votes
3 replies
192 views
Best practice for combining Ambient RNA correction and sc.pp.regress_out() in scRNA-seq
how-to scrna-seq ambient
written by messy_cat • messy_cat
0 votes
4 replies
281 views
Best approaches to identify pathways uniquely affected by different drugs?
pathway enrichment drugs transcriptomics
updated by ATpoint ATpoint • written by fnepo • fnepo
0 votes
1 reply
83 views
How should duplicate samples be handled when identifying super-enhancers?
macs2 superenhancer h3k27ac
updated by Bastien Hervé Bastien Hervé • written by G.J.W • G.J.W
0 votes
0 replies
32 views
News: Webinar- Target discovery in Alzheimer’s: Linking causal biology with CNS expression
alzheimers bioinformatics targetdiscovery drugdiscovery
updated by GenoMax GenoMax • written by Nicole • Nicole
3 votes
1 reply
414 views
News: Free interactive bioinformatics course with browser terminal simulator and real datasets
rna-seq tutorial python
updated by GenoMax GenoMax • written by aadil • aadil
0 votes
3 replies
115 views
Is NeMO down for good?
databases
updated by GenoMax GenoMax • written by mk mk
0 votes
1 reply
1.3K views
How to change the number of seeds/predictions run by Alphafold
alphafold protein-structure alphafold2 structure-prediction protein-prediction
updated by Matic Broz • Matic Broz • written by umjpyw • umjpyw
0 votes
3 replies
163 views
Annotating spatial transcriptomic
spatial transcriptomic
updated by Bastien Hervé Bastien Hervé • written by Synat • Synat
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