This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
5 replies
3.0K views
Speed up Seurat FindClusters execution?
seurat
updated by GenoMax GenoMax • written by CTLong • CTLong
0 votes
0 replies
22 views
News: Online Course: Introduction to Deep Learning for Biologists | 23–27 November
deeplearning ai cnns machinelearning drugdiscovery
written by Physalia-courses Physalia-courses
0 votes
20 replies
618 views
Tool: An automation and orchestration tool - Need honest feedback
orchestration automation
written by Nenad • Nenad
618 votes
172 replies
231K views
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook training
updated by Biostar Biostar • written by Istvan Albert Istvan Albert
0 votes
7 replies
107 views
Tool: Public NCBI messy and incomplete metadata problem tool
metadata curation messy public ncbi
written by Vy • Vy
0 votes
5 replies
119 views
Struggling to download using SRA toolkit from an Accession list
ascession toolkit sra
updated by samuel.a.odonnell samuel.a.odonnell • written by SethJ • SethJ
0 votes
2 replies
71 views
Tool: New tool for narrowing difficult missense variant shortlists
software variant-annotation comparative-genomics missense
written by Lara Finley • Lara Finley
0 votes
0 replies
24 views
Getting node coverage with vg pack
pack vg
written by samuel.michel • samuel.michel
0 votes
0 replies
37 views
Tutorial: New educational resource: Visualizing CNVs and structural variants in IGV
igv ngs cnv
written by wakaruszka • wakaruszka
2 votes
0 replies
35 views
News: Single Cell & RNA-seq course & certification- Become an expert
bioinformatics rnaseq ngs singlecell
written by Nicole • Nicole
2 votes
3 replies
80 views
igv beginer question
alignment
updated by ATpoint ATpoint • written by jolie • jolie
1 vote
3 replies
448 views
Looking for some data visualization resources!
data-visualisation genomics igv
updated by wakaruszka • wakaruszka • written by sameer • sameer
0 votes
7 replies
1.2K views
Analyzing data of Sanger sequencing
sangersequencing
updated by Nicole • Nicole • written by priyankasolanki • priyankasolanki
0 votes
1 reply
31 views
No ssDNA-reporter cleavage in Cas12a collateral cleavage assay- what are possible causes
crispr lbcas12a
updated by GenoMax GenoMax • written by Wenya • Wenya
0 votes
1 reply
45 views
How do I merge Framingham Heart Study phenotype data from BioLINCC with genotype data from dbGaP using participant IDs?
biolincc framingham dbgap genotype phenotype
updated by SeqBench • SeqBench • written by Krishalls • Krishalls
2 votes
1 reply
85 views
Appropriate Hardy-Weinberg Exact Test Alternative for Detecting Candidate Lethal Alleles with Missing Homozygotes?
r snp statistics hardy-weinberg population-genetics
updated by SeqBench • SeqBench • written by jhonatan.henrique • jhonatan.henrique
0 votes
1 reply
42 views
cBioPortal vs UCSC Xena — when to use which, and what are the actual pros/cons?
cbioportal tcga r xenabrownser
updated by SeqBench • SeqBench • written by Kelly • Kelly
0 votes
1 reply
36 views
How should recombinant haplotypes from vg haplotypes personalized GBZ be exported as FASTA?
vg
updated by Jouni Sirén Jouni Sirén • written by Etenesh • Etenesh
2 votes
2 replies
2.2K views
Forum: Cataloguing available spatial transcriptomics tools, then linking them together into a workflow?
cytassist transcriptomics nanostring xenium visium
updated by Olivia • Olivia • written by LauferVA LauferVA
0 votes
4 replies
135 views
De novo assembly for phylogenetic analysis
phylogenetics genomics
updated by shelkmike shelkmike • written by isag • isag
0 votes
0 replies
34 views
News: Causal AI Methods for Computational Biology – Online Course | 2–6 November
causalinference computationalbiology machinelearning ai
written by Physalia-courses Physalia-courses
0 votes
9 replies
227 views
News: I wrote a beginner-friendly book on AI in Biology, would love this community's thoughts
book biology ai
written by aadil • aadil
0 votes
0 replies
56 views
Tool: BIOSZEN: an R/Shiny package for Excel-based data analysis and visualization
data-visualization growth-curves data-analysis statistics microbiology
written by Pinkus • Pinkus
0 votes
1 reply
755 views
Purpose and necessity of removing PCR duplicates in m6A-seq analysis
pcr merip-seq m6a-seq duplicates
updated by SeqBench • SeqBench • written by remagen • remagen
2 votes
4 replies
1.5K views
PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
pacbio minimap2 alignment variants pbmm2
updated by SeqBench • SeqBench • written by louisflower1999 • louisflower1999
0 votes
4 replies
923 views
Convert Sanger FASTA for Y-STR marker into block-by-block repeat counts (motif structure), not just total repeats
y-str sanger fasta
updated by SeqBench • SeqBench • written by sue • sue
0 votes
1 reply
351 views
Cannot trim primers in R2 reads no matter what orientation of primers I use.
cutadapt
updated by SeqBench • SeqBench • written by DNAngel DNAngel
0 votes
1 reply
90 views
Job: Looking for a bioinformatics researcher to review a single-cell computational methodology
trajectory-inference rna-velocity cellrank single-cell scrna-seq
written by Matteo • Matteo
0 votes
2 replies
851 views
Download metabolic information from databases using the NCBI Taxonomy ID
metabolism database r taxonomy ncbi
updated by Giulio • Giulio • written by ThaiosX195 • ThaiosX195
0 votes
0 replies
35 views
How should I select inner and outer radii for dual-scale spatial niche analysis of Xenium tumor data?
xenium
written by zhentao • zhentao
0 votes
1 reply
52 views
multiBigwigSummary
wig bigwig multibigwigsummary
updated by Arup Ghosh Arup Ghosh • written by sk_24 • sk_24
0 votes
0 replies
60 views
Job: Sequencing Job Announcement - Forensic Science
ngs sequencing vacancy forensic job
written by Michael • Michael
0 votes
0 replies
29 views
News: Online live course: Putting protein structure into phylogenetic inference
phylogenetics protein
written by soledad.esteban • soledad.esteban
2 votes
1 reply
52 views
Differential expression in pseudobulk snRNA-seq with non-independent pseudobulks
rna-seq deseq2 single-cell expression differential
updated by GenoMax GenoMax • written by gttg • gttg
0 votes
1 reply
127 views
Transcript to gene file for Kallisto in a iso-seq transcriptome with no reference genome?
iso-seq kallisto
updated by SeqBench • SeqBench • written by bptrx • bptrx
0 votes
1 reply
95 views
PFAM double entry for the same PFAM accession with overlapping amino acids, how to keep only one?
interpro domains pfam functional
updated by SeqBench • SeqBench • written by ieie • ieie
0 votes
1 reply
113 views
High chrY call rates for human female 30x WGS samples, what am I doing wrong?
gatk plink chromosomes sex callrate
updated by SeqBench • SeqBench • written by Joel Wallenius Joel Wallenius
0 votes
3 replies
151 views
mob_suite doesn't recognize a plasmid I know is in the sequence
plasmid mob_suite
updated by SeqBench • SeqBench • written by blur blur
0 votes
3 replies
1.0K views
NTC amplification close to expected amplicon size during primer validation – primer-dimer or non-specific product?
ntc primer-design qpcr pcr
updated by SeqBench • SeqBench • written by Sashinika • Sashinika
0 votes
0 replies
38 views
News: online course: Machine Learning for Computational Cancer Genomics
machinelearning cancergenomics precisionmedicine
written by Physalia-courses Physalia-courses
1 vote
1 reply
2.6K views
VCF files and Bed tools
vcf bedtools
updated by vickybhai4206 • vickybhai4206 • written by Rna-Seq • Rna-Seq
0 votes
1 reply
108 views
What are the best alternatives to ROC-AUC for validating transcriptomic/gene expression signatures?
roc auc
updated by SeqBench • SeqBench • written by Pumla • Pumla
0 votes
1 reply
65 views
AI / ML sequence based mRNA half life prediction
halflife mrna ai ml
updated by SeqBench • SeqBench • written by petergrahamclark • petergrahamclark
0 votes
1 reply
57 views
How to subset features (genes, peaks, cells) scientifically when analyzing single cell multiomics dataset (scRNA-seq + scATAC-seq)?
multi-omics single-cell r
updated by SeqBench • SeqBench • written by KABILAN • KABILAN
0 votes
1 reply
83 views
Handling paired before/after microbiome data
samples paired
updated by SeqBench • SeqBench • written by benkosta • benkosta
0 votes
1 reply
62 views
MAGeCK MLE design matrix
mageck-mle pooled-screen mageck crispr-screen design-matrix
updated by SeqBench • SeqBench • written by Matthew • Matthew
0 votes
1 reply
86 views
WGCNA time course study
longitudinal wgcna
updated by SeqBench • SeqBench • written by Amit • Amit
0 votes
1 reply
63 views
Unexpected read structure in Ribo-seq libraries prepared with the QIAseq miRNA kit: missing 5′ adapter, 12 variable bases, and very short GC-rich inserts
riboseq
updated by SeqBench • SeqBench • written by GiovannaPrezia • GiovannaPrezia
1 vote
1 reply
71 views
What is the correct experimental unit: plot or plant in a randomized complete block design?
experimental design
updated by SeqBench • SeqBench • written by Dunia Aurora • Dunia Aurora
0 votes
1 reply
66 views
Is vg giraffe appropriate for RADseq sequencing reads?
vg radseq
updated by GenoMax GenoMax • written by RianeZ • RianeZ
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