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0 votes
3 replies
243 views
Reproducing ERCC spike-in correlation from public cfRNA data
rna-seq
updated by Istvan Albert 10K • | written by MJ Cho 0
0 votes
7 replies
624 views
DGEA using scRNA seq data.
seurat dgea seq scrna
updated by nmabbasi 0 • | written by yadavsoumya647 2
2 votes
8 replies
663 views
Tool: In-memory streaming downloader for massive NCBI/EBI datasets (bypasses disk I/O)
streaming download python tool pipeline
updated by GenoMax 16K • | written by Valentin Zhukovetski 2
0 votes
1 reply
194 views
Read depth & Biological replicates
read_depth biological_replicates
updated by OmnibusX 13 • | written by himanshu0102 1
0 votes
4 replies
415 views
Confused with EdgeR TMM normalization
edger normalization tmm rnaseq
written by joelking 0
1 vote
3 replies
950 views
Cell-cell communication for Visium HD
visium spatial visiumhd omics
updated by OmnibusX 13 • | written by fifty_fifty 10
1 vote
1 reply
301 views
Anyone else using VisiumHD data to do ligand-receptor inference analysis?
ligand-receptor visiumhd spatial-transcriptomics cell-cell-communication
updated by OmnibusX 13 • | written by danielpintard 2
0 votes
2 replies
417 views
Cell-type-specific markers across datasets
gene snrnaseq seurat findallmarkers
updated by OmnibusX 13 • | written by Chlogst 0
2 votes
14 replies
3.5K views
GUI commercial software for 10x single cell gene expression analysis
single-cell software commercial gui
updated by OmnibusX 13 • | written by firestar 173
0 votes
0 replies
160 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 1
2 votes
0 replies
187 views
Tutorial: Install and Setup ReadStore - The Open Source Database for NGS dataset
fastq
written by jonathan.alles 2
0 votes
0 replies
147 views
News: online course: AI for Genomics: From CNNs and LSTMs to Transformers (7–9 April)
genomics machinelearning ai deeplearning
written by Physalia-courses 281
0 votes
0 replies
93 views
Guide for interpreting somatic DNA alterations in cancer using ABSOLUTE?
copy-number-variation absolute
written by DdogBoss 7
0 votes
1 reply
176 views
How to get host and virus UMI count per cell with Bacterial genome data?
integrated bacteriophage umi prophage rumen
written by San 0
1 vote
1 reply
155 views
Tool: SpliceMap - annotate splicing regulatory elements on GenBank files
splicing
updated by colindaven 844 • | written by maxwraae 1
0 votes
0 replies
116 views
News: Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data (SPMP02)
spatial omics
updated by GenoMax 16K • | written by oliverhooker 14
2 votes
0 replies
109 views
News: Avoiding late-stage drug discovery failure with single-cell data
single-cell webinar discovery
written by beatriz.grum 2
2 votes
0 replies
126 views
News: From ‘Omics to Insights
omicsdata bioinformatics dataanalysis
written by Ana Carolina Reis 1
1 vote
0 replies
148 views
News: Single-cell RNA-seq, cell hashing and spatial transcriptomics
singlecell spatialtranscriptomics cellhashing
updated by GenoMax 16K • | written by Nicole 12
0 votes
0 replies
109 views
News: Spring School in Bioinformatics (9th edition) - ONLINE, 8–12 June
docker genomeassembly phylogenomics rnaseq
written by Physalia-courses 281
0 votes
1 reply
154 views
Denovo assembly in Bisulphite sequencing
mapping bisulphite denovo
updated by Ram 4.5K • | written by Smilesky 0
0 votes
11 replies
1.0K views
Tool: microBioRust: fast, lightweight bioinformatics for microbial genomics in Rust & Python
rust microbial bioinformatics python genomics
updated by Wayne 208 • | written by Lcrossman 2
0 votes
1 reply
275 views
MACS2 `--keep-dup all` parameter produces 10x more peaks
macs2 duplicates
updated by ATpoint 9.1K • | written by Aspire 43
1 vote
1 reply
250 views
Repetitive sequences multimapping handling
sequences repetitive
updated by kalavattam 85 • | written by frarodmar17 4
0 votes
5 replies
815 views
Substitution model selection with IQ-TREE (ModelFinder)
selction iq-tree modelfinder model substitution
updated by Mensur Dlakic 3.0K • | written by D 0
4 votes
0 replies
355 views
Tool: cnsplots: Generate Cell, Nature, and Science quality plots in Python with zero configuration
python
updated by ATpoint 9.1K • | written by Farid 4
0 votes
4 replies
741 views
Why is the full path required when creating a symlink in Linux?
linux symlink command-line offtopic
updated by kalavattam 85 • | written by sumaiyaanne 0
0 votes
0 replies
229 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 1
0 votes
2 replies
373 views
Using the VST normalization rather than the DESeqDataSetFromMatrix function for DESeq2
normalization deseq2 rnaseq
written by pailloufat 0
0 votes
0 replies
199 views
Job: R&D Manager Position at Vgenomics India
genomics bioinformatics genetics researcher
updated by Ram 4.5K • | written by sameer 4
0 votes
0 replies
151 views
News: Integrating Large Language Model Tools into R Workflows (Online course)
llms ai r
written by Physalia-courses 281
0 votes
4 replies
488 views
How to process Omni-C data for genome assembly
omni-c verkko assembly genome
updated by kalavattam 85 • | written by andrea 0
1 vote
1 reply
520 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 680 • | written by VPs 1
0 votes
3 replies
367 views
How is yeast extract and spent yeast SO much more nutritious than yeast?
offtopic yeast food fermentation
updated by Istvan Albert 10K • | written by kastabollen 0
0 votes
0 replies
167 views
News: Workshop: Introduction to R, May 15 - July 31, 2026 (10 weeks)
virtualworkshop uconn
written by zsc25001 1
2 votes
6 replies
2.6K views
How can I extract base and read name based on position from bam file?
bam sam genotype
updated by fravadona 0 • | written by gh 2
0 votes
12 replies
6.8K views
Extract read sequence from BAM files depending on the alignment coordinates
rna-seq
updated by fravadona 0 • | written by caggtaagtat 194
0 votes
0 replies
205 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 1
1 vote
9 replies
7.1K views
Extract reads from bam based on start coordinate
alignment
updated by fravadona 0 • | written by fizoca 1
0 votes
0 replies
182 views
News: Bioinformatics with Python courses
data-visualisation python ai programming
written by Physalia-courses 281
0 votes
1 reply
469 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 16K • | written by SD 0
0 votes
1 reply
264 views
wombat covariance estimation
wombat covariance
written by Bushra Bibi 8
0 votes
0 replies
136 views
Trait ontology database for wheat to check gene–trait associations ?
trait-ontology gene-id annotation wheat genomics
written by Sony Nguyen 2
0 votes
4 replies
501 views
Human Skin WGS Metagenome Sequence Quality Control
metagenomic_quality_control ngs_quality_control ngs metagenomics
written by Savindu 0
0 votes
1 reply
304 views
Job: Postdoctoral Position in circular RNA transcriptomics in Alzheimer’s disease
jobopening
updated by Ram 4.5K • | written by apooja 0
0 votes
1 reply
308 views
Job: Postdoctoral Positions in Proteomics and multiomics in Neurodegeneration
jobopening
updated by Ram 4.5K • | written by apooja 0
0 votes
1 reply
254 views
ELISA
elisa offtopic
updated by Ram 4.5K • | written by María José 1
0 votes
1 reply
195 views
sc.pl.heatmap absolute or relative expression?
scanpy scrna-seq expression heatmap
updated by ATpoint 9.1K • | written by npont 3
0 votes
0 replies
178 views
Batch correction on expression counts for deconvolution
deconvolution cellxgene batch-correction
updated by Ram 4.5K • | written by Jelka 0
0 votes
5 replies
512 views
Chimeric scaffolds in SPAdes assemblies
assemblies fungal spades
written by SomeOne 33
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