This is a test version of Biostars. For the public version, visit https://www.biostars.org.
1 vote
0 replies
390 views
Tool: Jowna: A pure web baed alternative to Krona for hierarchical data visualization
krona visualizer
written by Gianni • Gianni
0 votes
1 reply
289 views
Condensing/Combining samples of same condition into one VCF
variant vcf vcftools calling
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Shay • Shay
0 votes
0 replies
166 views
Finding Conserved, High-Coverage Windows in Transposable Elements for RNAi
read shrna elements coverage transposable
written by manikin_python9f • manikin_python9f
0 votes
1 reply
296 views
Plot mutations and read coverage in bacterial genomes
plot mutations coverage sequencing r
updated by colindaven colindaven • written by Paul • Paul
0 votes
1 reply
284 views
Forum: Recent M.S. bioinformatics grad seeking hands-on experience and advice
genomics career transcriptomics internship rna-seq
updated by ATpoint ATpoint • written by ravjolt • ravjolt
8 votes
16 replies
6.4K views
What Do You Use For Publication Alerts?
updated by Dimitris Grigoriadis • Dimitris Grigoriadis • written by Lee Katz Lee Katz
0 votes
1 reply
414 views
Forum: Will anyone want to use a PyDESeq2-based platform? How to improve my platform
rna-seq pydeseq2 volcano plot
updated by Istvan Albert Istvan Albert • written by Chuang, D-H • Chuang, D-H
0 votes
1 reply
290 views
nf-core bioinformatics hackathon
bioinformaticshackathon hackathon nfcore
updated by Pierre Lindenbaum Pierre Lindenbaum • written by rachana • rachana
0 votes
0 replies
173 views
News: Course: Handling Missing Data in R (Online, 22–24 April)
imputation missingdata r
written by Physalia-courses Physalia-courses
0 votes
5 replies
803 views
Estimate transposable elements copies and proportions
star transposons salmon
updated by samuel.a.odonnell samuel.a.odonnell • written by pailloufat • pailloufat
0 votes
9 replies
1.1K views
Tool: Jetomics: A private, no-code desktop platform for RNA-Seq analysis
rna-seq software windows transcriptomics
updated by benformatics benformatics • written by Aram Donyaee • Aram Donyaee
0 votes
1 reply
321 views
How to export high-resolution figures from QIIME2 visualizations for publication?
qiime2
updated by GenoMax GenoMax • written by Pluton17 • Pluton17
0 votes
5 replies
740 views
Denovo assembly oxford nanopore
nanopore assembly
updated by dr_cfoster dr_cfoster • written by Anam Saleem • Anam Saleem
0 votes
5 replies
650 views
Batch correction of scRNA using Scanorama
tumor immune scrnaseq batch_correction
written by mrashad mrashad
0 votes
0 replies
190 views
How to deal with high LD in bacterial genomes for selection scans.
bacteria gxe genome
written by nitinra • nitinra
1 vote
5 replies
1.4K views
Job: Database developer to University of Copenhagen
developer programming database bioinformatics python
written by info info
0 votes
4 replies
765 views
How can I search for orthologs ?
blast hmmer ortholog
updated by dulankak • dulankak • written by D • D
0 votes
1 reply
328 views
CPU-based prediction of multi-protein complexes
interactions prediction protein-complex protein-protein
updated by dthorbur dthorbur • written by ja569116 • ja569116
0 votes
12 replies
1.5K views
Which correlation test better for small ordinal data
ordinal correlation data test
updated by kalavattam • kalavattam • written by MS • MS
0 votes
2 replies
482 views
why my fastqc on trimmed data failed?
fastqc galaxy analyses ngs
updated by Ram Ram • written by kamran.kouchakzadeh.kk • kamran.kouchakzadeh.kk
0 votes
4 replies
857 views
Forum: Courses on RNA-seq focussing on statistical analysis and design
rna-seq
written by microfuge microfuge
0 votes
1 reply
348 views
What's the best way to batch retrieve RefSeq accession numbers from a list of type strains?
refseq type strains genomes
updated by GenoMax GenoMax • written by Mackenna • Mackenna
0 votes
1 reply
394 views
Preparing a bed file for showing gene structure(exon/intron) by GSDS from a list of gene ID
bed
updated by cmdcolin cmdcolin • written by HajiNasrollah • HajiNasrollah
0 votes
0 replies
378 views
News: AI for Genomics course - online, 7–9 April
genomics machinelearning ai deeplearning
written by Physalia-courses Physalia-courses
0 votes
3 replies
707 views
Significant Kallisto index size difference: v0.51.0 (550MB) vs v0.48.0 (2.6GB)
kallisto
updated by GenoMax GenoMax • written by musfirajamil • musfirajamil
0 votes
0 replies
298 views
Well-established methods to distinguish malignant vs normal epithelial cells in mouse scRNA-seq data (10x Chromium)
scrnaseq
written by andromeda.milky42 • andromeda.milky42
0 votes
4 replies
802 views
Should I treat different assemblies of a sample as different "haplotypes"?
hifi uncertainty assembly
updated by Istvan Albert Istvan Albert • written by Panos Panos
0 votes
0 replies
277 views
background choice in HOMER motif enrichment
motif homer
written by sarahmanderni sarahmanderni
5 votes
15 replies
3.3K views
Tool: FastAlign: 3x Faster Sequence Alignment on Commercial CPUs with 100% BWA-MEM Compatibility
sequece alignment genome analysis
written by YeWen • YeWen
0 votes
4 replies
837 views
Chip Seq Analysis of RNA Polymerase 2
chipseq
updated by theodore theodore • written by Gaurav • Gaurav
0 votes
1 reply
361 views
.KO files on IMG don't have headers
ko kegg orthologies img
updated by Arup Ghosh Arup Ghosh • written by rlpeng • rlpeng
7 votes
7 replies
2.3K views
Tool: AliNe (Alignment in Nextflow)
nextflow alignment
updated by Istvan Albert Istvan Albert • written by Juke34 Juke34
0 votes
0 replies
243 views
News: Assembly and Annotation of Genomes course - online, 9-13 March
genomeassembly genomeannotation nanopore pacbio illumina
written by Physalia-courses Physalia-courses
0 votes
6 replies
1.1K views
Detecting effects of DNA base modifications by NGS
nanopore pod5 bacteria promethion
written by zizigolu zizigolu
1 vote
0 replies
229 views
How "bases mapped (cigar)" value in samtools stats is calculated?
samtools
written by Tian • Tian
0 votes
3 replies
915 views
No significant genes after FDR correction in microarray (n=3) – how to proceed with exploratory analysis?
microarray limma
updated by Ram Ram • written by Samaksh • Samaksh
0 votes
3 replies
1.0K views
Recommended thresholds for filtering modkit pileup bedMethyl output (Nmod, fraction_modified, Nfail)
methylation modkit bedmethyl
updated by GenoMax GenoMax • written by alexandrakortsi • alexandrakortsi
1 vote
6 replies
11K views
How to make a summary plot like below?
cancer classes oncoplots
updated by selkamand • selkamand • written by Jianlan • Jianlan
1 vote
1 reply
925 views
High log2 fold change but no significant adjusted p-values in DESeq2 (two conditions, three biological replicates each)
adjusted-p-values deseq2 rna-seq
updated by ATpoint ATpoint • written by Chamara Lakshitha • Chamara Lakshitha
0 votes
1 reply
1.1K views
Understand Bedtools coverage output
bedtools coverage
updated by kalavattam • kalavattam • written by ramshahaya • ramshahaya
1 vote
0 replies
249 views
Variant Alelle Frequency graph interpretation
cnv vaf
updated by GenoMax GenoMax • written by 715c719f • 715c719f
2 votes
1 reply
1.6K views
Tool: Modernized RNA-MuTect pipeline for tumor-only RNA-seq somatic variant calling
somatic rna-seq
updated by Charlotte Stubbe • Charlotte Stubbe • written by darklings darklings
0 votes
4 replies
815 views
U2OS cell line reference genome
reference alignment
written by anubratadas • anubratadas
0 votes
2 replies
661 views
What is the most commonly used .aln viewer?
alignment msa
updated by cmdcolin cmdcolin • written by yesquokkan • yesquokkan
0 votes
2 replies
721 views
GATK resource bundle alternatives
hg38 gatk resource bundle
updated by GenoMax GenoMax • written by stlba • stlba
0 votes
3 replies
2.6K views
How do you do differential splicing using edgeR command diffSpliceDGE?
differential-splicing diffsplicedge edger
updated by Gordon Smyth Gordon Smyth • written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
0 replies
314 views
Job: Postdoc Opportunities: Cancer Genomics for Regulatory RNA Therapeutics
postdoc
written by rory.johnson • rory.johnson
0 votes
1 reply
396 views
PyMOL surface coloring problem in TCR-MHC contact visualization
tcrcontactresidue pymol tcr
updated by Mensur Dlakic Mensur Dlakic • written by rachana • rachana
0 votes
0 replies
241 views
News: Course - Epigenomics Data Analysis (4th edition), online, 13–17 April
rnaseq atacseq epigenomics multiomics chipseq
written by Physalia-courses Physalia-courses
0 votes
0 replies
391 views
Job: Postdoctoral Bioinformatician / Computational Biologist (m/f/d)
job posting
updated by colindaven colindaven • written by lalit.kaurani • lalit.kaurani
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