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0 votes
1 reply
2.1K views
Using adonis to include a random effect
mixed-model adonis
updated by LChart LChart • written by leranwangcs • leranwangcs
0 votes
3 replies
2.0K views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix regression
updated by LChart LChart • written by leranwangcs • leranwangcs
0 votes
2 replies
1.2K views
Can I compare kallisto counts from samples with different amount of reads?
rna-seq kallisto
written by bioinfo • bioinfo
0 votes
1 reply
1.3K views
How to get the reference panel sites for TOPMed hg37 and 38
imputation
updated by bk11 • bk11 • written by sinhas • sinhas
0 votes
5 replies
1.5K views
Best way to deal with overlapping read names in merged BAM files
picard markduplicates
written by shpak.max • shpak.max
0 votes
1 reply
862 views
merging Seurat objects after SCT
seurat sct
updated by Ram Ram • written by michelle.swarovski • michelle.swarovski
0 votes
1 reply
876 views
Two databases: Human Microbiome Project and MGnify
microbiome databases
updated by GenoMax GenoMax • written by haiying.kong haiying.kong
0 votes
2 replies
993 views
RNAseq 1 control 2 different treatment
rna-seq
written by matteo.levorato • matteo.levorato
1 vote
0 replies
557 views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
gene-ontology rna-seq r
updated by Ram Ram • written by Oscar • Oscar
0 votes
2 replies
2.2K views
CombineGVCFs vs. MergeVcfs
combinegvcfs mergevcfs gatk wgs gvcf
updated by Jeremy Leipzig Jeremy Leipzig • written by Sd • Sd
0 votes
0 replies
542 views
News: Deadline Approaching: PETs for Public Health Challenge
privacy public-health-challenge
updated by Ram Ram • written by polarise polarise
0 votes
2 replies
1.3K views
Problem with Sniffles pipeline and SV calling help
sv sniffles structuralvariant
updated by GenoMax GenoMax • written by njornet • njornet
6 votes
0 replies
994 views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
written by Biostar Biostar
0 votes
1 reply
1.3K views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
gsea pathways go-terms
updated by i.sudbery i.sudbery • written by Manko47 • Manko47
1 vote
6 replies
1.6K views
Odd results with BLAST remote
blast remote ncbi
updated by b.contreras.moreira • b.contreras.moreira • written by Begonia_pavonina • Begonia_pavonina
3 votes
9 replies
3.7K views
BRAKER3 genome annotation
annotation braker3 genome
updated by andorjkiss • andorjkiss • written by manaswiniparija3 • manaswiniparija3
2 votes
0 replies
635 views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
smiles
written by Alexander • Alexander
1 vote
6 replies
1.7K views
Do I need to go back and filter my long-reads?
alignment nanopore filtering qc ont
updated by GenoMax GenoMax • written by eebloom • eebloom
0 votes
0 replies
535 views
Automated internal stop codon checker
orf stopcodon internal virus
written by Balazs Horvath • Balazs Horvath
0 votes
0 replies
574 views
Repeat expansion identification tools for long-read data
fragilex repeatexpansion long-read fmr1
written by adarsh • adarsh
0 votes
4 replies
2.2K views
Which command ro run MAKER pipeline for gene annotation ?
run. command to makerpipeline.
updated by GenoMax GenoMax • written by Sony Nguyen • Sony Nguyen
0 votes
0 replies
709 views
FreeBayes detection capacity
reads freebayes long
written by quentinperriere • quentinperriere
0 votes
2 replies
1.1K views
VCF annotation with gnomADv4 using R package
annotation gnomadv4 r vcf
written by DKA • DKA
0 votes
7 replies
4.9K views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
career advice
updated by Dunois • Dunois • written by AdviceSeeker • AdviceSeeker
0 votes
0 replies
620 views
Plotting heatmap of genes in each samples scRNA in Seurat
scrna heatmap
written by Hien • Hien
0 votes
2 replies
1.2K views
Merging Outputs from plink --assoc and --hardy to Produce Table
plink pandas r
written by Koketso • Koketso
0 votes
3 replies
2.0K views
Extracting data from a local NCBI taxonomy database
r ncbi xml e-utilities blast
updated by josev.die • josev.die • written by Begonia_pavonina • Begonia_pavonina
0 votes
0 replies
942 views
Novel cyclic peptide structure prediction
protein structure-prediction alphafold peptide
updated by Ram Ram • written by menyawino • menyawino
0 votes
0 replies
582 views
News: Online course: Network Analysis in R
networkanalyis r
written by Physalia-courses Physalia-courses
0 votes
3 replies
2.0K views
Ensembl gene id conversion
biomart ensembl
updated by ATpoint ATpoint • written by naveedhasan2000 • naveedhasan2000
0 votes
2 replies
1.4K views
Extracting information from gff3 file produced by augustus
augustus gff3
updated by Istvan Albert Istvan Albert • written by Jiang • Jiang
83 votes
24 replies
33K views
Tutorial: Gene Set Enrichment Analysis
microarray enrichment rna-seq gsea
updated by Gordon • Gordon • written by Hamid Ghaedi Hamid Ghaedi
0 votes
3 replies
1.3K views
Deseq2 : Paired analysis or otherwise
linear-regression paired-analysis deseq2 longitudinal-analysis
updated by ATpoint ATpoint • written by IM • IM
1 vote
1 reply
940 views
How to highlight genes on genome visual reprezentation/what tool to use?
gene genome
updated by Alex Reynolds Alex Reynolds • written by shiksha • shiksha
0 votes
1 reply
1.3K views
adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features
gtf gff transcript cds exon
updated by Pratik Pratik • written by Sadik Muzemil • Sadik Muzemil
0 votes
0 replies
511 views
Different flagstat number after using MergeBamAlignment
mergebamalignment samtools flagstat
written by ThomasLam • ThomasLam
0 votes
4 replies
1.9K views
How to download large-scale cDNA sequences from NCBI effectively ?
ncbi. cdna
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Sony Nguyen • Sony Nguyen
0 votes
0 replies
1.4K views
Core SNP tree VS. concatenated core genome tree
phylogenetic tree snp
written by YiweiZhu • YiweiZhu
0 votes
9 replies
15K views
Genome assembly statistical tools
assembly statistics
updated by skdv2522 • skdv2522 • written by margab • margab
0 votes
6 replies
2.2K views
Ciriquant not configuring hisat2 indexed files
ciriquant
written by Atul K. • Atul K.
1 vote
1 reply
1.2K views
How to handle more than 1 SRA Run per Experiment?
sra preprocessing
updated by ATpoint ATpoint • written by Janmajay • Janmajay
0 votes
2 replies
1.3K views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
written by O.rka O.rka
0 votes
6 replies
2.2K views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
written by Dunois • Dunois
0 votes
1 reply
969 views
How do I identify gene duplication or paralogs in an annotated reference genome assembly
blast duplication paralog genome
updated by san96 • san96 • written by brimaloney24 • brimaloney24
1 vote
7 replies
2.1K views
DESeq2 Multifactor Design
rna-seq deseq2
updated by Ram Ram • written by AHerik • AHerik
1 vote
5 replies
2.2K views
Blacklist for bacterial genome [ChIPseq]?
chipseq blacklist
updated by Ram Ram • written by Emily Wasson • Emily Wasson
0 votes
0 replies
733 views
SeuratDisk: including "counts" dataset in conversion to AnnData
seurat seuratdisk anndata
updated by Ram Ram • written by roussine • roussine
0 votes
0 replies
591 views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
atac-seq homer
written by Ronin • Ronin
1 vote
4 replies
4.7K views
How do I install plink2 on a mac?
plink2 plink
updated by zx8754 zx8754 • written by emilija.romic • emilija.romic
0 votes
5 replies
1.6K views
Is it possible to set different tracks to the same scale in JBrowse
track jbrowse
updated by Ram Ram • written by Jose • Jose
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