This is a test version of Biostars. For the public version, visit https://www.biostars.org.
5 votes
4 replies
302 views
Tool: Run edgeR, limma, and clusterProfiler from Python - pandas in, pandas out
python enrichment edger limma deseq2
updated by Gordon Smyth Gordon Smyth • written by John • John
0 votes
3 replies
257 views
sample size for pangenome project
size pangenome sample
written by Thuong • Thuong
0 votes
5 replies
321 views
Tool: Giving Bulk-RNA Seq Analysis Tool (QC, Deseq2, GSEA, Cell Lines, etc) for free so the lovely community can test it
rna-seq rna bioinformatics bulk-rna
updated by kalavattam • kalavattam • written by Abdullah - NotchBio • Abdullah - NotchBio
2 votes
5 replies
307 views
Tool: I built BioMark — like Geekbench but for bioinformatics. Tells you honestly if your laptop can run BWA-MEM2, STAR, Cell Ranger and more. No tools needed.
bioinformatics python hardware wes benchmark
updated by Istvan Albert Istvan Albert • written by shahbazigenomics • shahbazigenomics
1 vote
2 replies
132 views
NCBI SQN: table2asn doesn't include my transcriptID correctly
sqn annotation ncbi genome
written by Heleen • Heleen
0 votes
2 replies
165 views
How do I consider that my reads might map to the 3' UTR (3'-tag RNA seq)?
rna-seq
updated by Ram Ram • written by applepeanut • applepeanut
0 votes
2 replies
176 views
Best practices for cross-species differential expression analysis
microarray rna cross-species deg
updated by Ram Ram • written by fnepo • fnepo
0 votes
3 replies
217 views
Forum: Contribute and learn in open source projects
open-source
updated by jared.andrews07 jared.andrews07 • written by Andy • Andy
0 votes
1 reply
128 views
using igv-reports for large dataset
vcf wgs igv
updated by Arup Ghosh Arup Ghosh • written by question_log • question_log
0 votes
5 replies
293 views
A genome impossible to be assembled
assembling genomics yeast genome
updated by colindaven colindaven • written by dafunny99 • dafunny99
0 votes
0 replies
148 views
Job: Postdoctoral Researcher (AI & Genomics)
microbiome genomics machinelearning single-cell
written by mtabaka • mtabaka
0 votes
2 replies
146 views
Single-cell Proteomics
sc proteomics
updated by kalavattam • kalavattam • written by iibrams07 • iibrams07
0 votes
1 reply
156 views
what Trimmomatic parameters would you recommend for RNA-seq data ?
alternative trimmomatic splicing rna-seq
updated by kalavattam • kalavattam • written by mahsa80.mm • mahsa80.mm
0 votes
2 replies
1.2K views
RNA-seq raw counts normalization for survival analysis
survival tcga rna-seq r
updated by ATpoint ATpoint • written by fifty_fifty • fifty_fifty
1 vote
2 replies
2.5K views
Import Pubchem Compound Sdfs Into Oracle?
updated by allice12jame.s • allice12jame.s • written by jocsch • jocsch
0 votes
0 replies
99 views
Tool: Allelix – opens source offline variant annotation against 7 public databases (ClinVar, gnomAD, PharmGKB, GWAS Catalog, SNPedia, AlphaMissense, CADD)
python pharmacogenomics clinvar vcf annotation
written by dial481 • dial481
2 votes
5 replies
289 views
RNA-seq with multiple treatment groups: Do I need additional correction across contrasts?
experimental multiple testing statistics design rna-seq
written by Netanel • Netanel
0 votes
3 replies
225 views
Fast QC per base sequence problem
fastqc
written by Duy • Duy
1 vote
0 replies
90 views
Tool: Pipette.bio - a conversational AI agent that runs real bioinformatics analyses
biology bioinformatics computational llm agent
written by chirag • chirag
0 votes
4 replies
292 views
Blog: How I caught a problematic RNA-seq sample before it ruined my differential expression analysis
rna-seq rna pca qc
updated by Ram Ram • written by Abdullah - NotchBio • Abdullah - NotchBio
0 votes
0 replies
65 views
News: Online course: Big Data Phylogeny and Comparative Methods
bigdataphylogeny comparativegenomics r
written by Physalia-courses Physalia-courses
0 votes
2 replies
165 views
Is this library suitable for sequencing?
library ngs rna-seq
updated by GenoMax GenoMax • written by Poshan • Poshan
0 votes
1 reply
91 views
How are novel Snippy-derived mutations typically handled in bacterial WGS studies without wet-lab validation?
microbial-genomics snippy mutation
updated by Arup Ghosh Arup Ghosh • written by lavslipoprotein2204 • lavslipoprotein2204
0 votes
2 replies
145 views
Tool: A new pilot project for genomics analysis — AriaDNA
fasta viewer sequences visualization
written by davidmaimoun • davidmaimoun
10 votes
12 replies
4.4K views
Tool: Announcing bioSyntax: Syntax highlighting for biological files
computational-biology
updated by GenoMax GenoMax • written by anicet.ebou anicet.ebou
0 votes
1 reply
94 views
single RNA integration
snrna 10x smartseq2 scrna
updated by ATpoint ATpoint • written by mrashad mrashad
0 votes
0 replies
41 views
Illegal instruction error when running GSNAP
gsnap gmap dump core
written by artemisdiscovery • artemisdiscovery
0 votes
0 replies
52 views
Theoretical Idea: Modeling a surface-display cellulase system in human gut bacteria
synthetic-biology
written by DoGoodGetGood09 • DoGoodGetGood09
0 votes
0 replies
56 views
Covariate shift in gene expression datasets
expression bioinformatics gene
written by Hargunjeet • Hargunjeet
0 votes
0 replies
52 views
Tool: Tool to recover missing / inconsistent NCBI metadata - feedback welcome
metadata curation ncbi
written by Vy • Vy
0 votes
2 replies
133 views
Need immediate help with Docking
autodock bioinformatics project docking
updated by chirag • chirag • written by Shreyashi • Shreyashi
0 votes
1 reply
93 views
Forum: Need suggestion / roadmaps for bio informatics as a Computer science student
roadmap tutorial advice help
updated by GenoMax GenoMax • written by Anuj • Anuj
0 votes
0 replies
86 views
Tutorial: ABodyBuilder2 on macOS: OMP Error #15 libomp.dylib already initialized (Abort trap: 6)
abodybuilder macos immunebuilder conda
updated by Arup Ghosh Arup Ghosh • written by parthivrajesh • parthivrajesh
0 votes
2 replies
155 views
Reproducing a published rice salt-stress RNA-seq analysis from FASTQ: feedback on workflow choices?
agent ai rnaseq fastq
written by chirag • chirag
0 votes
1 reply
113 views
Purchasing Biostars Handbook
handbook biostars
updated by GenoMax GenoMax • written by Anis • Anis
0 votes
0 replies
39 views
News: Workshop in Berlin- Agent-based and Individual-based modelling using NetLogo - 24-28 August
netlogo ibm abm
written by Physalia-courses Physalia-courses
0 votes
2 replies
201 views
Best strategy for WGCNA with small sample numbers across multiple conditions
network wgcna
updated by pixie@bioinfo pixie@bioinfo • written by María José • María José
0 votes
0 replies
70 views
Global vs per layer normalization and scaling in Seurat workflow
seurat data normalisation integration singlecell
written by luca8650 • luca8650
0 votes
0 replies
57 views
News: Writing a grant or preparing a manuscript? Make sure your biological story is backed by strong evidence and clear visualizations.
discovery omics publication grantwriting pathways
written by Nicole • Nicole
0 votes
2 replies
152 views
Biological replicates: individual samples or pooled samples for small RNA-seq?
mirna-seq pooling
updated by GenoMax GenoMax • written by Cristina Zamora • Cristina Zamora
0 votes
0 replies
53 views
Real-time pathogen / microbial detection from raw nanopore signals (no basecalling) ?
edge-computing pathogen-detection raw-signal-analysis nanopore-sequencing genomics
written by klenehan123 • klenehan123
0 votes
2 replies
159 views
Question about Blast
blast
updated by Wayne Wayne • written by testbotrr • testbotrr
0 votes
2 replies
191 views
raw matrices or filtered matrices
cellranger snrnaseq
updated by Ryeo Jae • Ryeo Jae • written by Zee • Zee
1 vote
4 replies
457 views
Forum: Building an open-source LIMS project to better understand lab and bioinformatics workflows
software python lims
written by Eduardo • Eduardo
0 votes
0 replies
48 views
How to place telomeric unassigned contigs (acrocentric p‑arms) back onto chromosomes in a Verkko assembly
genome-assembly t2t verkko telomeres scaffolding
written by andrea • andrea
0 votes
9 replies
4.6K views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
featurecounts lowassignedreads star
updated by ATpoint ATpoint • written by beginner123 • beginner123
0 votes
2 replies
196 views
Forum: How do you disclose LLM/agent use in code and documentation?
ethics authorship agent attribution llm
updated by jared.andrews07 jared.andrews07 • written by kalavattam • kalavattam
0 votes
3 replies
1.5K views
Tool to merge two GTFs
r gtf
updated by Abdullah - NotchBio • Abdullah - NotchBio • written by manninm • manninm
0 votes
13 replies
708 views
Noise vs signal in RNA-seq.
atg star coverage rna-seq
updated by Aditya • Aditya • written by Shakunthala Natarajan • Shakunthala Natarajan
1 vote
8 replies
467 views
Forum: Transitioning from bioinformatics to data engineering - advice needed
career transition entrylevel
updated by Abdullah - NotchBio • Abdullah - NotchBio • written by eyaggelia146 • eyaggelia146
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