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0 votes
0 replies
95 views
Trait ontology database for wheat to check gene–trait associations ?
trait-ontology gene-id annotation wheat genomics
written by Sony Nguyen • Sony Nguyen
0 votes
4 replies
451 views
Human Skin WGS Metagenome Sequence Quality Control
metagenomic_quality_control ngs_quality_control ngs metagenomics
written by Savindu • Savindu
0 votes
1 reply
241 views
Job: Postdoctoral Position in circular RNA transcriptomics in Alzheimer’s disease
jobopening
updated by Ram Ram • written by apooja • apooja
0 votes
1 reply
260 views
Job: Postdoctoral Positions in Proteomics and multiomics in Neurodegeneration
jobopening
updated by Ram Ram • written by apooja • apooja
0 votes
1 reply
203 views
ELISA
elisa offtopic
updated by Ram Ram • written by María José • María José
0 votes
1 reply
171 views
sc.pl.heatmap absolute or relative expression?
scanpy scrna-seq expression heatmap
updated by ATpoint ATpoint • written by npont • npont
0 votes
0 replies
148 views
Batch correction on expression counts for deconvolution
deconvolution cellxgene batch-correction
updated by Ram Ram • written by Jelka • Jelka
0 votes
5 replies
450 views
Chimeric scaffolds in SPAdes assemblies
assemblies fungal spades
written by SomeOne • SomeOne
1 vote
1 reply
294 views
DESeq2 gives high sig gene number
deseq2 tcga
updated by ATpoint ATpoint • written by Sara • Sara
0 votes
3 replies
354 views
How do I merge two overlapping rbcL FASTA fragments in BioEdit?
alignment chloroplast sanger
updated by lieven.sterck lieven.sterck • written by alnus • alnus
0 votes
2 replies
514 views
BCLConvert 4.x behavior when Lane is omitted from [BCLConvert_Data] — per-lane defaults or single pool?
samplesheet bcl2fastq illumina sequencing bclconvert
written by Chaitanya • Chaitanya
0 votes
0 replies
102 views
Best tool to orient a protein complex before SMD in GROMACS
moleculardynamics gromacs smd steeredmoleculardynamics orientation
written by rachana • rachana
1 vote
4 replies
1.2K views
Hello, I analyzed ONT 16S amplicon data using the EPI2ME workflow with Minimap2, but the output does not include representative FASTA sequences needed for downstream functional prediction with PICRUSt
epi2me picrust2 16s metagenomic ont
updated by Leonardo • Leonardo • written by Ramen • Ramen
0 votes
1 reply
176 views
mismatch sites from GAM/GAF
vg
updated by colindaven colindaven • written by zhengluo • zhengluo
1 vote
3 replies
558 views
Is it normal and ok to observe symmetric PCA & heatmap when correcting paired samples for the patient ID?
differential-expression-analysis paired-deseq2
updated by i.sudbery i.sudbery • written by marieke • marieke
1 vote
1 reply
220 views
Statistical test for separation of groups in PCA and DESeq2 design with confounders
bulk rna desq2
updated by shannonNorgenBiotek • shannonNorgenBiotek • written by archanaverma433 • archanaverma433
0 votes
1 reply
338 views
Should I pool counts from the X and Y copies of pseudoautosomal genes when performing differential expression analysis?
pseudoautosomal differential-expression annotation
updated by Gordon Smyth Gordon Smyth • written by Ryan • Ryan
0 votes
4 replies
597 views
Weak overlap of cell states of scRNAseq and Xenium data of the same samples
xenium
written by Beginner • Beginner
0 votes
0 replies
243 views
Low-coverage NGS CNV: multiple chromosomes showing ~2.3 copy number with low confidence — mosaicism or normalization artifact?
pgt cnv
written by Alison • Alison
0 votes
2 replies
1.6K views
How do I compare two similar PPI networks using Cytoscape?
cytoscape string ppi networks
updated by Midsummer • Midsummer • written by gemmalouisebaldock • gemmalouisebaldock
0 votes
2 replies
280 views
Forum: Complexity in reproduce the research work
bioinformatics researcher reproducibility
updated by Ram Ram • written by Muhammad • Muhammad
0 votes
2 replies
255 views
Protein Homologous Sequences!
proteomics vaccinology immunoinformatics
updated by Ram Ram • written by Muhammad • Muhammad
0 votes
4 replies
576 views
FindTransferAnchors error: "No features to use in finding transfer anchors" when using CELLxGENE `.h5ad` reference with Seurat
scanpy seurat scrnaseq findtransferanchors
written by VPs • VPs
0 votes
0 replies
117 views
News: (online course) Fundamentals of Biostatistics with R - 13–17 April
biomedicalresearch biostatistics epidemiology survivalanalysis
written by Physalia-courses Physalia-courses
0 votes
0 replies
126 views
BLUPF90+....
blup
written by hwangseok1025 • hwangseok1025
7 votes
0 replies
263 views
Tool: polars-bio - blazing fast Python DataFrames for genomic operations
genomics dataframes python polars
written by Marek • Marek
0 votes
1 reply
232 views
Exploring project idea
validation structural svs variants
updated by dthorbur dthorbur • written by mustafa.kpn • mustafa.kpn
0 votes
0 replies
155 views
tcga data analysis correlation between two signature
correlation signature gene tcga
written by jerko.ljubetic • jerko.ljubetic
0 votes
1 reply
280 views
Handling high missingness when merging single-sample VCFs
wgs ultima_wgs vcf merge
updated by samuel.a.odonnell samuel.a.odonnell • written by SeoG • SeoG
1 vote
3 replies
476 views
metagenome binning with MetaBAT2, and Maxbin2 created bins for some samples but not others.
bacteria fungi metagenome binning
updated by Mensur Dlakic Mensur Dlakic • written by Irshad • Irshad
0 votes
1 reply
269 views
RNA_MUTECT_1.0_1 not working
variant tumor-only rna_mutect somatic
updated by DdogBoss • DdogBoss • written by Charlotte Stubbe • Charlotte Stubbe
0 votes
2 replies
389 views
Forum: MS CS after BS in Bioinformatics
csit
written by anasjamshed anasjamshed
0 votes
7 replies
3.3K views
Gene Set Enrichment Analysis with RNA-seq data
rna-seq next-gen r
updated by Gordon Smyth Gordon Smyth • written by deepak18 • deepak18
1 vote
3 replies
724 views
Tool: rsfgsea: Rust implementation of preranked GSEA built for large transcriptome workflows where GSEA became the bottleneck
rust python gsea tool fgsea
written by Denis Demin • Denis Demin
2 votes
1 reply
354 views
Tool: Fast and Accurate DeepVariant on native Linux ARM64. Costs less than a piece of gum per genome
deepvariant arm64 variant-calling
updated by cmdcolin cmdcolin • written by antoniolamb • antoniolamb
1 vote
5 replies
2.7K views
Extraction of read subsequences based on a region from a sam file
alignment sequence
updated by fravadona • fravadona • written by gordon.freeman • gordon.freeman
0 votes
0 replies
124 views
News: (Online course) Metabarcoding in Microbial Ecology (16–20 March)
qiime2 metabarcoding r microbial-ecology
written by Physalia-courses Physalia-courses
0 votes
2 replies
316 views
"Exome" probes designed off of mRNA sequences
capture exome sequencing
written by Shay • Shay
0 votes
0 replies
115 views
How to Interpret PHEWAS hits that are very rare but very significant?
frequency phenotype allele phewas p-value
written by joshua.rubin • joshua.rubin
0 votes
0 replies
228 views
Job: Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
genetics bioinformatics alzheimer omics
updated by GenoMax GenoMax • written by belloy • belloy
0 votes
0 replies
189 views
Very high number of unique sequences in PacBio full-length 16S CCS data using DADA2
pacbio dada2 microbiome amplicon 16s
written by muhammad.ali • muhammad.ali
0 votes
1 reply
252 views
Phylogenetic tree construction
phylogenetic tree
updated by Michael Dondrup Michael Dondrup • written by Vishy001 • Vishy001
0 votes
1 reply
1.1K views
Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation
funcotator mutect2 tmb rna-mutect-wmn rna-mutect
updated by Charlotte Stubbe • Charlotte Stubbe • written by kim • kim
0 votes
3 replies
581 views
MM39 BED Files Genome Features
bed mm39
updated by GenoMax GenoMax • written by joseph.landry • joseph.landry
0 votes
0 replies
181 views
News: UConn CBC: de novo RNA-seq & scRNA-seq March workshops
scrnaseq workshop rnaseq training
written by bioadam • bioadam
0 votes
4 replies
506 views
UCSC Genome Browser: Custom Data?
browser genome ucsc
written by Shane • Shane
0 votes
1 reply
340 views
V3V4 16s Sequencing, lots of merged reads that are too short
v3v4 16s dada2
updated by michael.ante michael.ante • written by Emilie • Emilie
0 votes
1 reply
295 views
Generating .rnk file for GSEA
gsea
updated by mbyvcm mbyvcm • written by Siobhan • Siobhan
0 votes
1 reply
443 views
Seurat v5 workflow for Integrated data
findallmarkers seurat dataintegration sctransform layers
updated by Arup Ghosh Arup Ghosh • written by _deb • _deb
0 votes
2 replies
417 views
High mapping failure (>80%) in clusterProfiler::bitr after HIPPIE–MCODE workflow
hippie cytoscape mcode
written by SD • SD
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