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0 votes
4 replies
1.3K views
gene annotation tool recommendations for oomycetes
oomycetes annotation
updated by lieven.sterck 1.6K • | written by colindaven 844
1 vote
15 replies
6.8K views
STAR aligner - Is this still maintained?
star aligner rnaseq
updated by GenoMax 16K • | written by Joshi 1
0 votes
4 replies
1.9K views
Does anyone know how to transform the following transcript ID's from TCGA isoform data
ucsc isoform tcga
updated by Zhenyu Zhang 130 • | written by B.N. 1
0 votes
0 replies
609 views
eQTL Analysis for Structural Variants (SV) – Seeking Relevant Software
eqtl sv
written by chiyong4783 0
0 votes
1 reply
811 views
Building pangenome graphs in minigraph-cactus using vcf?
pangenome vcf cactus
updated by Mark 173 • | written by Uveyik 8
0 votes
2 replies
1.3K views
RSEM and STAR
star rnaseq rsem
written by rajdeepboral00 7
0 votes
0 replies
581 views
Interpretaion of tensorQTL output for ieQTL analysis
tensorqtl ieqtl beta-values
updated by Ram 4.5K • | written by cool.aditya286 0
0 votes
6 replies
2.6K views
How to compare gene prediction
gene-prediction
updated by lieven.sterck 1.6K • | written by Acervo 0
0 votes
0 replies
679 views
ArchR extending gene activity till nearest promoter
archr addgenescoremat
written by Bastien Hervé 680
0 votes
0 replies
480 views
Heritability
greml heritability
written by am29 6
0 votes
1 reply
606 views
Transcriptome Reconstruction for Transcript Discovery
taco stringtie
updated by michael.ante 408 • | written by Emy Alade 4
0 votes
2 replies
967 views
Having trouble running Desktop version of Pse-in-One
pse-in-one dna
written by George 3
0 votes
1 reply
763 views
Comparison of different gene catalog abundance
assembly catalog metagenome illumina gene
updated by mark.ziemann 199 • | written by young_bioinformatician 25
0 votes
1 reply
1.5K views
Nothing happens when running GATK VCF Validate Variants. Output warning: processed 0 (zero) total variants
gatk vcf snp validatevariants
updated by Pierre Lindenbaum 17K • | written by maikejet 0
0 votes
3 replies
1.4K views
Annotate GWAS result gene function from GFF file
gwas gff gff3 annotation
updated by lieven.sterck 1.6K • | written by alnus 0
0 votes
0 replies
560 views
WGCNA sample-data preprocessing order
gene-expression wcgna microarray network data-preprocessing
written by Reuben 0
0 votes
3 replies
2.9K views
drug sensitivity prediction
deseq2 oncopredict r drug
updated by Luka 0 • | written by luffy 13
0 votes
1 reply
738 views
VCFfiltering
vcf bcftools freebayes
updated by Mark 173 • | written by Peter 0
0 votes
0 replies
526 views
Analysis and Verification of Mathematical Equations in the Theory of Consciousness
consciousness brian neuron neurobiology
updated by GenoMax 16K • | written by steklolampa 0
0 votes
0 replies
600 views
Genetic Trio Phasing with EAGLE2 using hg38
trios haplotype phasing genetics
written by heskett 11
0 votes
3 replies
1.6K views
b37 liftover
b37 liftover
written by spesks 0
0 votes
0 replies
822 views
Plugging output files from phyluce phasing workflow into Structure
phyluce uce bam phasing structure
written by gabe.somarriba 0
0 votes
0 replies
711 views
gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
header pacbio bam basecaller gcpp
written by therosng 0
0 votes
1 reply
888 views
circos ignoring the ticks and plots
diagram circos
updated by GenoMax 16K • | written by baibhu1234 6
0 votes
4 replies
2.0K views
Strange offsetting in deeptools?
deeptools
written by Elijah 1
0 votes
4 replies
1.4K views
Merging gvcf files between Dragen and other calling tools
gvcf merge bcftools
written by tacrolimus 15
0 votes
6 replies
2.4K views
Download SRA raw data using efetch
sra-toolkit efetch biopython
written by biofysikos 0
0 votes
7 replies
2.0K views
Issue with CIBERSORTx Error 139
cibersortx docker error193
updated by jared.andrews07 1.9K • | written by Hamdache 0
0 votes
0 replies
740 views
Repeat Modeler Database Generation
masker modeler genome fungus repeat
written by SomeOne 33
0 votes
1 reply
890 views
How to scale data matrix in Seurat
scale
updated by marco.barr 22 • | written by frarodmar17 4
0 votes
1 reply
971 views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly genoem fungus hic sequencing
updated by GenoMax 16K • | written by SomeOne 33
0 votes
1 reply
721 views
Box plot of gene expression data
boxplot
updated by ATpoint 9.1K • | written by a.stef.44 1
0 votes
4 replies
3.0K views
Questions regarding GSEA - clusterProfiler
rna-seq gsea
updated by Irshad 1 • | written by CaroH 1
0 votes
0 replies
668 views
Account for Clinical Variables in RNA-Seq Analysis
edger batch effect
written by fabian 1
0 votes
4 replies
1.6K views
bioinformatics tutorial on Oxford Nanopore Technologies
oxford nanopore
updated by GenoMax 16K • | written by Bogdan 144
6 votes
0 replies
1.7K views
Tutorial: Step by step tutorial to replicate a genomics figure
r unix chip-seq bioconductor
written by Ming Tommy Tang 469
0 votes
0 replies
628 views
How to determine which pangenome nodes correspond to hg38 coordinates?
pangenome reference-genome hg38 genomics
written by a5864557 1
0 votes
0 replies
517 views
LDhat analysis pipeline
recombination ldhat
written by chaudharyc61 12
0 votes
7 replies
2.6K views
Parsing error in sam file when converting to bam
samtools bwa fastq bam sam
updated by GenoMax 16K • | written by emily.coger 0
4 votes
1 reply
1.6K views
GATK site filtering: when should I use VQSR or hard filtering?
vqsr gatk
updated by alba 1 • | written by samuelandjw 27
0 votes
1 reply
944 views
Missing `pro_ref` Folder in PICRUSt2 Default Files
github picrust2
updated by Ram 4.5K • | written by ameeraelshinawy 0
0 votes
1 reply
1.1K views
How to Display Metadata on IGV Visualizations
integrative-genomics-viewer igv
updated by Ram 4.5K • | written by luminea 2
0 votes
3 replies
1.3K views
Understanding how to deal with Brain snRNA-seq data
scanpy python single-cell anndata rna
updated by Ming Tommy Tang 469 • | written by AlexStar 22
0 votes
2 replies
1.3K views
RNA-seq combined treatment interaction experiment design
rna-seq deseq2
updated by Ram 4.5K • | written by Manko47 1
0 votes
0 replies
1.2K views
Forum: Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping variants
updated by GenoMax 16K • | written by Ian 614
10 votes
11 replies
25K views
CIBERSORT deconvolution advice
cibersort cibersortx deconvolution
updated by Nguyen 0 • | written by joker33 15
0 votes
1 reply
1.2K views
News: In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
transcriptomics workshop rna-seq
written by ecSeq Bioinformatics 9
0 votes
0 replies
661 views
Sesame Data ExperimentHub and related issues
caching sesame methylation
updated by GenoMax 16K • | written by jain72744 1
0 votes
0 replies
758 views
Unable to link peaks to genes for multiomics data
multiome multiomics linkpeaks signac 10x
written by sribas.chowdhury888 0
0 votes
0 replies
585 views
GWAS for Klebsiella isolates
technical help gwas
written by Bahnie 0
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