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0 votes
2 replies
519 views
Creating Gene Ontology (GO) plot
go analysis r
written by HajiNasrollah • HajiNasrollah
0 votes
1 reply
392 views
Best approach for miRNA-seq when species is not in miRBase
mirbase mirna
updated by GenoMax GenoMax • written by ki • ki
0 votes
3 replies
501 views
Protein structure complex data-bases
e f
updated by Ram Ram • written by Diksha • Diksha
0 votes
0 replies
462 views
Ambient RNA correction when most of the ambient comes from a specific cell type of interest
seurat single-cell cellbender single-nuclei ambient
written by txema.heredia • txema.heredia
0 votes
4 replies
530 views
GEO search - automatization
geo
updated by Bharat K. C. Patel • Bharat K. C. Patel • written by pinheirofabiano • pinheirofabiano
0 votes
1 reply
449 views
AVITI vs Illumina - Replicate Concordance
illumina sequencing. aviti amplicon
updated by GenoMax GenoMax • written by adina • adina
0 votes
0 replies
362 views
Harmonising WGS and SNP array data
data handling array snp wgs
written by FB1999 • FB1999
0 votes
1 reply
421 views
News: AI in Drug Discovery - online, 12–15 October
machinelearning drugdiscovery deeplearning gnns ai
written by Physalia-courses Physalia-courses
0 votes
1 reply
394 views
Proteomics normalization: equal protein loading but unequal cell counts in clinical samples
proteomics
updated by ATpoint ATpoint • written by Kittinun • Kittinun
0 votes
8 replies
1.4K views
Querry Error - Can't connect to MySQL server on '127.0.0.1' (111)
annotation biomart error
updated by AFerr • AFerr • written by Claire • Claire
0 votes
1 reply
469 views
Troubleshooting High cis/tran ratio in Hi-C
sequencing hi-c
updated by i.sudbery i.sudbery • written by HT • HT
0 votes
0 replies
381 views
Tool: kegg-mcp-server-python: an open-source Python MCP server for querying KEGG from AI assistants
api mcp kegg ai python
updated by GenoMax GenoMax • written by lucasservi • lucasservi
0 votes
9 replies
716 views
How to run Spades with debug option
debug assembly spades
updated by Michael Dondrup Michael Dondrup • written by marongiu.luigi marongiu.luigi
0 votes
0 replies
346 views
News: Online course - Spatial Omics in R/Bioconductor - 18–20 May.
spatialomics bioconductor r
written by Physalia-courses Physalia-courses
0 votes
3 replies
2.4K views
Databases to check variant pathogenicity
wholeexomesequencing
updated by Agasthya • Agasthya • written by Fatemeh Nabizadeh • Fatemeh Nabizadeh
0 votes
0 replies
372 views
News: EMBO Practical Course | Causality in biomedicine: going beyond associations
bioinformatics training biomedicine
written by EMBL Events EMBL Events
0 votes
4 replies
608 views
How to set fq.gz as input for bbduk (BBmap)?
preprocessing bbmap sequencing trimming
updated by fernando • fernando • written by marongiu.luigi marongiu.luigi
1 vote
6 replies
1.0K views
Best practices for improving BRAKER annotation with long-read Iso-Seq and short-read RNA-seq transcriptome data
braker non-model genome-annotation iso-seq rna-seq
updated by fernando • fernando • written by Andrei Makhon • Andrei Makhon
0 votes
1 reply
361 views
Best OrgDb for phytoplankton
bioconductor rvvgo orgdb
updated by fernando • fernando • written by Teleo • Teleo
0 votes
8 replies
808 views
Non-specific annotations in KEGG, Pfam for plant denovo RNA seq data
plant novo rna seq de
updated by fernando • fernando • written by Hemangi • Hemangi
0 votes
7 replies
786 views
How to extract headers from protein fasta file for seqkit analysis?
signalp subsetting seqkit headers faa
updated by fernando • fernando • written by marongiu.luigi marongiu.luigi
1 vote
8 replies
767 views
DESeq2- comparing treatments in repeated experiment
batch-effect deseq2
updated by fernando • fernando • written by Jade • Jade
0 votes
12 replies
999 views
Poly-G and Missing data Novaseq X vs Novaseq 6000
poly-g gbs novaseqx missingdata
updated by GenoMax GenoMax • written by Butterfly • Butterfly
0 votes
7 replies
561 views
Conflicting Genome Sizes from GenomeScope2.0 and Assembler
assembly genome genomescope2 abyss
written by saamhasan55 • saamhasan55
0 votes
0 replies
383 views
Tool: VarViz: A Free, Open-Source Web Application for Protein-Centric Missense Variant Visualization and Automated ACMG/AMP Classification
missense clinvar acmg variant_interpretation gnomad
written by Agasthya • Agasthya
1 vote
3 replies
230 views
How do you know if a sequencing dataset is safe to run before pipelines?
sequencing ngs quality-control fastq pipelines
updated by lieven.sterck lieven.sterck • written by johndains • johndains
2 votes
0 replies
211 views
Job: Bioinformatics Postdoc -University of Louisville
bioinformatics multi-omics biology computational
written by uofbccbioinformatics • uofbccbioinformatics
0 votes
3 replies
268 views
Unable to build vg from source: `fatal error: opening dependency file bdsg/obj/eades_algorithm.d: No such file or directory`
vg
updated by fernando • fernando • written by pmenzel+www.biostars.org • pmenzel+www.biostars.org
0 votes
8 replies
495 views
Best contrast strategy to identify condition-specific effects in limma
rna differential expression drugs limma
written by fnepo • fnepo
0 votes
2 replies
223 views
How to retrieve RNA expression dataset of METABRIC - 144 adjacent normal samples ?
metabric
updated by fernando • fernando • written by pooja • pooja
2 votes
1 reply
120 views
When to use RSEM vs z-scores in cBioPortal mRNA data?
rna-seq cbioportal
updated by fernando • fernando • written by Kelly • Kelly
2 votes
1 reply
106 views
Mitochondrial DNA analysis (illumina global array)
microarray heteroplasmy illumina mitochondria
updated by fernando • fernando • written by 112233 • 112233
0 votes
2 replies
177 views
Questions about karyotyping and metaphase spread
chromosome karyotyping
updated by fernando • fernando • written by SF • SF
0 votes
7 replies
612 views
Three possible copies of One Gene, which one is true?
gene copies
updated by fernando • fernando • written by Gabriel • Gabriel
0 votes
1 reply
67 views
“Handling diversity saturation in soil microbiome data: alternatives to standard alpha diversity indices?”
diversity-alpha-diversity-microbiome-ecology-phylogenetics-statistics-analysis
updated by fernando • fernando • written by gautamyam673 • gautamyam673
0 votes
2 replies
170 views
Downstream analysis for microarray data
microarray affymetrix limma
updated by fernando • fernando • written by Qistina • Qistina
0 votes
3 replies
259 views
Continuous Cox survival analysis with TCGA gene expression data?
mrna tcga cox univariate survival
updated by fernando • fernando • written by maartje • maartje
0 votes
1 reply
94 views
WGCNA soft thresholding: R² plateau at power 2 but mean connectivity drops to near zero by power 3 . Unusual pattern?
wgcna
updated by fernando • fernando • written by Isadora • Isadora
0 votes
2 replies
181 views
Per base sequence content of Metagenomic samples
metagenomics ngs fastqc
updated by fernando • fernando • written by Savindu • Savindu
0 votes
7 replies
468 views
Doubt about single Cell Data integration
10x single cell harmonization integration
updated by ATpoint ATpoint • written by ijarne • ijarne
0 votes
1 reply
86 views
IntegrateData orig.ident = "SeuratObject"
integration seurat sctransform st
updated by fernando • fernando • written by mmorillo • mmorillo
0 votes
1 reply
120 views
Different QC strategies for ONT reads in read-based vs assembly-based metagenomics
metagenomics ont assembly nanopore
written by Luwell • Luwell
0 votes
1 reply
93 views
SCEVAN analysis for the scRNA datasets
cnv integration scrna
updated by fernando • fernando • written by mrashad mrashad
0 votes
2 replies
258 views
Low overlap due to poor reverse read quality in 2×300 bp V3–V4 amplicon sequencing (DADA2)
metagenome dada2
updated by fernando • fernando • written by yesquokkan • yesquokkan
0 votes
1 reply
451 views
When should I use JoinLayers() after merging multiple Seurat objects?
single cell seurat
updated by fernando • fernando • written by 城玮 • 城玮
0 votes
1 reply
146 views
Clustering of RNA-seq data
normalization rna-seq clustering
updated by fernando • fernando • written by Eduardo • Eduardo
0 votes
2 replies
97 views
Very less highly expressed genes in DGE analysis
dge analysis
updated by fernando • fernando • written by ziraa • ziraa
0 votes
5 replies
398 views
External identity on Terra in Europe with NIH
terra dbgap gsutil
updated by fernando • fernando • written by Charlotte Stubbe • Charlotte Stubbe
0 votes
4 replies
364 views
Large FASTQ file processing failure: MetaPhlAn 3.0.7 + HUMAnN on 16-core 64GB system
metagenomics biobakery metaphlan3.0.7 humann3
updated by fernando • fernando • written by chatterjeejayeeta100 • chatterjeejayeeta100
1 vote
2 replies
213 views
Recommended bwa-mem2 implementation for Illumina short-read alignment?
ngs bwa-mem2 alignment illumina
updated by fernando • fernando • written by kalavattam • kalavattam
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