This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
0 replies
19 views
WGCNA: Should seed tissues be included with root and shoot samples when studying nitrate uptake in maize?
rnaseq wgcna plant biology transcriptomics co-expression
written by mugwimbi 0
0 votes
1 reply
48 views
Tool: I built a browser-based toolkit for common bioinformatics and molecular biology tasks - looking for feedback
molecular-biology bioinformatics software sequence-analysis web-tools
updated by Michael Dondrup 5.6K • | written by Ravi 0
0 votes
1 reply
55 views
News: Registration closing soon: 2nd Berlin Winter School in RNA-Seq Data Analysis, November 2–5, 2026
rnaseq transcriptomics workshop
written by ecSeq Bioinformatics 9
0 votes
0 replies
24 views
PAML codeml fails with exit status 1
paml dnds phylogenomics
written by Md Hasibul 0
624 votes
174 replies
232K views
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated by Biostar 380 • | written by Istvan Albert 10K
1 vote
1 reply
848 views
Job: Applications Now Open – Summer 2026 Teaching Opportunities [SSPI]
temporary stem summer jobs paid
updated by Henry 2 • | written by Emaly 1
0 votes
5 replies
8.1K views
bcftools mpileup --max depth : What would be a reasonable setting for this option?
bcftools mpileup consensus
updated by pnrmm 6 • | written by VBer 21
0 votes
1 reply
39 views
Tool: ExomeFlow: reproducible WES analysis from paired FASTQs to annotated variants
bioinformatics
updated by Pierre Lindenbaum 17K • | written by Robin 0
0 votes
1 reply
34 views
Tool: ATGCFLOW: web-based FASTQ-to-variant workflow with annotation and review - feedback requested
bioinformatics
updated by Pierre Lindenbaum 17K • | written by Robin 0
0 votes
0 replies
26 views
Job: Assistant Professor in Computational and Experimental Molecular Biology
molecular-biology professor faculty
written by UCSDBioSci 3
2 votes
3 replies
64 views
Difficulty separating cell types in Parse Biosciences scRNA-seq data compared with 10x Genomics
scrna-seq transcriptome parsebiosciences
updated by ATpoint 9.1K • | written by Nitin Narwade 168
0 votes
1 reply
63 views
How to set a cutoff TPM value to determine whether a gene is expressed or not?
value tpm expression gene
updated by ATpoint 9.1K • | written by Muhammad Tahmid 0
0 votes
1 reply
59 views
Looking someone experienced in genomics/bioinformatics to help guide me through applying AlphaGenome
bioinformatics
written by entrepreneurshipa 0
0 votes
0 replies
42 views
Forum: Career advice
jobs advice bioinfo career
written by BionfoDevot 0
0 votes
2 replies
50 views
Molecular Loop ONT Demultiplexing
demultiplexing molecular ont loop
written by Tillie 0
6 votes
3 replies
76 views
Tool: GenomeSieve: a graphical tool for filtering and downloading NCBI genome assemblies
genome ncbi software bioinformatics
updated by jpcastrodarocha 0 • | written by davimcampos09 6
1 vote
7 replies
8.3K views
Merge vcf files of structural variants
structural_variants vcf merge
updated by Qingxiang 2 • | written by ma17 2
0 votes
2 replies
850 views
Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy
sv variant-calling vcf
updated by GenoMax 16K • | written by sardana.thakur.prachi 0
0 votes
0 replies
34 views
WGCNA removing mitochondria and ribosomal genes
wgcna
written by María José 1
4 votes
6 replies
2.9K views
Is there any gene nomenclature conversion tool that recognizes old names?
genomics r annotation
updated by GenoMax 16K • | written by emibaffo 7
0 votes
1 reply
43 views
Creating a custom reference with cellranger mkref for EBV B95-8: duplicate gene id
gtf cellranger mkref
updated by marco.barr 22 • | written by malcapi 0
0 votes
0 replies
31 views
News: COURSE: AI for Drug Discovery – Machine Learning, Deep Learning and Graph Neural Networks | 12–15 October
deeplearning ai cnns machinelearning drugdiscovery
written by Physalia-courses 281
0 votes
1 reply
71 views
Forum: Looking to gain any experience
student
updated by Arup Ghosh 402 • | written by Tafadzwa 0
2 votes
4 replies
121 views
exogenous gene in scRNA-sequencing
rna sequencing
updated by GenoMax 16K • | written by Morris_Chair 39
0 votes
0 replies
44 views
News: Workshop:Virtual Genome Assembly, Sept. 22-24, 2026
virtual genomeassembly uconn workshop
written by zsc25001 1
2 votes
0 replies
51 views
Tool: SwiftCNV — a python tool to infer copy number variations (CNVs) from single-cell RNA-seq data
scrna cnv infercnv python
written by adrianparrilla 2
1 vote
3 replies
140 views
Tool: GATES: automated whole-exome sequencing analysis for somatic and germline variant discovery
germline pathogenic somatic exome variant
updated by Cyriac Kandoth 609 • | written by Nicholas 2
1 vote
0 replies
68 views
News: Teaching bioinformatics differently: Applied Bioinformatics 2026
bioinformatics
written by Istvan Albert 10K
0 votes
3 replies
85 views
ClusterProfiler-enrichGO questions about the universe
enrichgo clusterprofiler
updated by jared.andrews07 1.9K • | written by Esperanza 0
2 votes
1 reply
82 views
Struggling to detect known partial deletion in NOTCH2 from WES (germline, small cohort, no reference panel) - CNV callers give inconsistent/wrong results
wesanalysis detectionofpartialdeletion
updated by Chris Miller 2.2K • | written by odi 3
0 votes
0 replies
49 views
News: Online live course - Agentic AI for Life Sciences - 3-4 December
agenticai genomics ai
written by Physalia-courses 281
0 votes
1 reply
65 views
Best practice for downstream processing of pig gene identifiers and human orthologues
analysis scrna pigs ensembl. sequencing
updated by mark.ziemann 199 • | written by Arindam 2
1 vote
3 replies
198 views
whole-genome sequencing of a non-model organism: from raw reads to genome assembly and gene annotation
genomic sequencing
updated by shelkmike 201 • | written by WUSCHEL 94
0 votes
0 replies
38 views
Question about vg giraffe haplotype sampling to genotype SVs in many samples
sv giraffe vg haplotype-sampling
updated by GenoMax 16K • | written by Alex Samano 0
0 votes
2 replies
83 views
Merging similar coordinates in Methylation data
methylation
written by 1769mkc 127
0 votes
4 replies
165 views
all samples are aligned vertically on the PCA
pca rna-seq
updated by ATpoint 9.1K • | written by marieke 1
0 votes
4 replies
169 views
Biopython Entrez.efetch returning empty FASTA file when fetching NCBI nucleotide sequences
fasta biopython entrez python ncbi
written by Suriya 2
0 votes
2 replies
143 views
scRNA-seq: does my DESeq2 and GSEA workflow make sense?
scrnaseq
updated by rfran010 174 • | written by juliya.k 0
0 votes
0 replies
54 views
Quality control benchmark for Sanger files
control quality sanger
written by Jean 0
2 votes
0 replies
77 views
News: AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome
alphagenome google
written by Pierre Lindenbaum 17K
2 votes
3 replies
227 views
News: is Biomart dead ? "We have frozen BioMart but it remains accessible via our archive servers."
ensembl
updated by Istvan Albert 10K • | written by Pierre Lindenbaum 17K
0 votes
2 replies
969 views
Understanding sctransform
sctransform seurat
updated by Phi 0 • | written by Deepak Tanwar 421
0 votes
1 reply
91 views
Many GEO CTCF ChIP-seq datasets have no controls: is there a different standard for CTCF ChIP-seq?
background controls chip-seq input ctcf
written by kalavattam 85
0 votes
0 replies
51 views
News: Online Course: Nextflow for Beginners – 9–11 November
reproducibility workflowmanager nextflow
written by Physalia-courses 281
0 votes
2 replies
152 views
is this DE analysis with edgeR correct?
edger transcriptomics help
updated by Gordon Smyth 916 • | written by Estefania Belen 0
0 votes
0 replies
45 views
How to get permutations or derivatives of a candidate molecule?
bioinformatics screening drug chemiinformatics
written by mark.ziemann 199
0 votes
1 reply
100 views
Forum: CHANGING CAREER: FROM EDUCATION TO BIOINFOMATICS FIELD
biostars
updated by ATpoint 9.1K • | written by Ngofira 0
35 votes
36 replies
18K views
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated by ashish 0 • | written by Ram 4.5K
0 votes
0 replies
43 views
Consultation: Multisample copyKAT visualization
bioinformatic methods analysis
written by 2795906776 0
0 votes
2 replies
126 views
Tool: spades-rs — a Rust port of SPAdes genome assembler (seeking feedback and benchmarking)
genome-assembly assembly ngs spades
written by Sagnik 1
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