This is a test version of Biostars. For the public version, visit https://www.biostars.org.
2 votes
7 replies
1.1K views
Help understanding best binning practices
binning viruses metagenome contigs
updated by 5heikki 5heikki • written by boone5jones • boone5jones
1 vote
0 replies
79 views
News: News: Exploring biological mechanisms without a dataset using IPA
bioinformatics qiagenipa dataanalysis omics
written by Gabi • Gabi
12 votes
17 replies
1.1K views
Tool: Daily Academic - Personalized scientific literature discovery
academic_discovery relevant_paper_discovery literature biorxiv_discovery web_app
written by Dimitris Grigoriadis • Dimitris Grigoriadis
0 votes
0 replies
92 views
News: Online Course: Epigenomics Data Analysis (13–17 April )
rnaseq atacseq hic chipseq multiomics
written by Physalia-courses Physalia-courses
0 votes
2 replies
244 views
Taxanomic classification of unpaired reads in paired-end read files with Kraken2 with --paired flag
metagenomics kraken2 taxanomic_classification ngs
written by Savindu • Savindu
2 votes
4 replies
360 views
Is the Canonical Transcript Really the Dominant Isoform?
gtex
updated by Istvan Albert Istvan Albert • written by Shicheng Guo Shicheng Guo
0 votes
0 replies
134 views
Job: PT lecturer in bioinformatics @ Tufts Biology
masters biostatistics teaching
written by Frank • Frank
1 vote
11 replies
6.9K views
RNA-SEQ where only a subset of genes is of interest
rna-seq deseq
updated by DriesB DriesB • written by Aspire Aspire
0 votes
3 replies
186 views
Reproducing ERCC spike-in correlation from public cfRNA data
rna-seq
updated by Istvan Albert Istvan Albert • written by MJ Cho • MJ Cho
0 votes
7 replies
434 views
DGEA using scRNA seq data.
seurat dgea seq scrna
updated by nmabbasi • nmabbasi • written by yadavsoumya647 • yadavsoumya647
2 votes
8 replies
556 views
Tool: In-memory streaming downloader for massive NCBI/EBI datasets (bypasses disk I/O)
streaming download python tool pipeline
updated by GenoMax GenoMax • written by Valentin Zhukovetski • Valentin Zhukovetski
0 votes
1 reply
156 views
Read depth & Biological replicates
read_depth biological_replicates
updated by OmnibusX • OmnibusX • written by himanshu0102 • himanshu0102
0 votes
4 replies
315 views
Confused with EdgeR TMM normalization
edger normalization tmm rnaseq
written by joelking • joelking
1 vote
3 replies
719 views
Cell-cell communication for Visium HD
visium spatial visiumhd omics
updated by OmnibusX • OmnibusX • written by fifty_fifty • fifty_fifty
1 vote
1 reply
227 views
Anyone else using VisiumHD data to do ligand-receptor inference analysis?
ligand-receptor visiumhd spatial-transcriptomics cell-cell-communication
updated by OmnibusX • OmnibusX • written by danielpintard • danielpintard
0 votes
2 replies
321 views
Cell-type-specific markers across datasets
gene snrnaseq seurat findallmarkers
updated by OmnibusX • OmnibusX • written by Chlogst • Chlogst
2 votes
14 replies
3.3K views
GUI commercial software for 10x single cell gene expression analysis
single-cell software commercial gui
updated by OmnibusX • OmnibusX • written by firestar firestar
0 votes
0 replies
121 views
Best way to quantify unstranded PCR-cDNA -seq with many multimappers and possible intronic signal?
reads long repeats multimappers
written by vanda.gaonach-lovejoy • vanda.gaonach-lovejoy
2 votes
0 replies
153 views
Tutorial: Install and Setup ReadStore - The Open Source Database for NGS dataset
fastq
written by jonathan.alles • jonathan.alles
0 votes
0 replies
107 views
News: online course: AI for Genomics: From CNNs and LSTMs to Transformers (7–9 April)
genomics machinelearning ai deeplearning
written by Physalia-courses Physalia-courses
0 votes
0 replies
63 views
Guide for interpreting somatic DNA alterations in cancer using ABSOLUTE?
copy-number-variation absolute
written by DdogBoss • DdogBoss
0 votes
1 reply
131 views
How to get host and virus UMI count per cell with Bacterial genome data?
integrated bacteriophage umi prophage rumen
written by San • San
1 vote
1 reply
113 views
Tool: SpliceMap - annotate splicing regulatory elements on GenBank files
splicing
updated by colindaven colindaven • written by maxwraae • maxwraae
0 votes
0 replies
72 views
News: Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data (SPMP02)
spatial omics
updated by GenoMax GenoMax • written by oliverhooker oliverhooker
2 votes
0 replies
77 views
News: Avoiding late-stage drug discovery failure with single-cell data
single-cell webinar discovery
written by beatriz.grum • beatriz.grum
2 votes
0 replies
91 views
News: From ‘Omics to Insights
omicsdata bioinformatics dataanalysis
written by Ana Carolina Reis • Ana Carolina Reis
1 vote
0 replies
109 views
News: Single-cell RNA-seq, cell hashing and spatial transcriptomics
singlecell spatialtranscriptomics cellhashing
updated by GenoMax GenoMax • written by Nicole • Nicole
0 votes
0 replies
69 views
News: Spring School in Bioinformatics (9th edition) - ONLINE, 8–12 June
docker genomeassembly phylogenomics rnaseq
written by Physalia-courses Physalia-courses
0 votes
1 reply
120 views
Denovo assembly in Bisulphite sequencing
mapping bisulphite denovo
updated by Ram Ram • written by Smilesky • Smilesky
0 votes
11 replies
873 views
Tool: microBioRust: fast, lightweight bioinformatics for microbial genomics in Rust & Python
rust microbial bioinformatics python genomics
updated by Wayne Wayne • written by Lcrossman • Lcrossman
0 votes
1 reply
216 views
MACS2 `--keep-dup all` parameter produces 10x more peaks
macs2 duplicates
updated by ATpoint ATpoint • written by Aspire Aspire
1 vote
1 reply
206 views
Repetitive sequences multimapping handling
sequences repetitive
updated by kalavattam • kalavattam • written by frarodmar17 • frarodmar17
0 votes
5 replies
680 views
Substitution model selection with IQ-TREE (ModelFinder)
selction iq-tree modelfinder model substitution
updated by Mensur Dlakic Mensur Dlakic • written by D • D
4 votes
0 replies
278 views
Tool: cnsplots: Generate Cell, Nature, and Science quality plots in Python with zero configuration
python
updated by ATpoint ATpoint • written by Farid • Farid
0 votes
4 replies
584 views
Why is the full path required when creating a symlink in Linux?
linux symlink command-line offtopic
updated by kalavattam • kalavattam • written by sumaiyaanne • sumaiyaanne
0 votes
0 replies
188 views
How do I normalise quality scores generated by different CNV callers for fair collapsing with Truvari?
cnv exome-sequencing cnv-calling sv-merging
written by yawolberg • yawolberg
0 votes
2 replies
307 views
Using the VST normalization rather than the DESeqDataSetFromMatrix function for DESeq2
normalization deseq2 rnaseq
written by pailloufat • pailloufat
0 votes
0 replies
152 views
Job: R&D Manager Position at Vgenomics India
genomics bioinformatics genetics researcher
updated by Ram Ram • written by sameer • sameer
0 votes
0 replies
114 views
News: Integrating Large Language Model Tools into R Workflows (Online course)
llms ai r
written by Physalia-courses Physalia-courses
0 votes
4 replies
418 views
How to process Omni-C data for genome assembly
omni-c verkko assembly genome
updated by kalavattam • kalavattam • written by andrea • andrea
1 vote
1 reply
459 views
FindAllMarkers() returns empty results in Seurat v5 object with multiple layers (~170k cells, Visium HD segmented cells)
visium findallmarkers scrnaseq visiumhd 10x
updated by Bastien Hervé Bastien Hervé • written by VPs • VPs
0 votes
3 replies
335 views
How is yeast extract and spent yeast SO much more nutritious than yeast?
offtopic yeast food fermentation
updated by Istvan Albert Istvan Albert • written by kastabollen • kastabollen
0 votes
0 replies
122 views
News: Workshop: Introduction to R, May 15 - July 31, 2026 (10 weeks)
virtualworkshop uconn
written by zsc25001 • zsc25001
2 votes
6 replies
2.5K views
How can I extract base and read name based on position from bam file?
bam sam genotype
updated by fravadona • fravadona • written by gh • gh
0 votes
12 replies
6.7K views
Extract read sequence from BAM files depending on the alignment coordinates
rna-seq
updated by fravadona • fravadona • written by caggtaagtat caggtaagtat
0 votes
0 replies
157 views
News: Call for Posters - CIBB 2026 (AI & Computational Intelligence for Bioinformatics and Biostatistics), Rome, Sept 2-4
bionformatics machine-learning artificial-intelligence genomics biostatistics
written by Umberto • Umberto
1 vote
9 replies
7.0K views
Extract reads from bam based on start coordinate
alignment
updated by fravadona • fravadona • written by fizoca • fizoca
0 votes
0 replies
127 views
News: Bioinformatics with Python courses
data-visualisation python ai programming
written by Physalia-courses Physalia-courses
0 votes
1 reply
416 views
Metadata details (Microns Per Pixel data-MPP) for Whole Slide Images (WSIs) downloaded from the TCGA
whole tcga images mpp slide
updated by GenoMax GenoMax • written by SD • SD
0 votes
1 reply
186 views
wombat covariance estimation
wombat covariance
written by Bushra Bibi Bushra Bibi
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