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0 votes
0 replies
729 views
Repeat Modeler Database Generation
masker modeler genome fungus repeat
written by SomeOne • SomeOne
0 votes
1 reply
865 views
How to scale data matrix in Seurat
scale
updated by marco.barr • marco.barr • written by frarodmar17 • frarodmar17
0 votes
1 reply
957 views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly genoem fungus hic sequencing
updated by GenoMax GenoMax • written by SomeOne • SomeOne
0 votes
1 reply
699 views
Box plot of gene expression data
boxplot
updated by ATpoint ATpoint • written by a.stef.44 • a.stef.44
0 votes
4 replies
3.0K views
Questions regarding GSEA - clusterProfiler
rna-seq gsea
updated by Irshad • Irshad • written by CaroH • CaroH
0 votes
0 replies
658 views
Account for Clinical Variables in RNA-Seq Analysis
edger batch effect
written by fabian • fabian
0 votes
4 replies
1.6K views
bioinformatics tutorial on Oxford Nanopore Technologies
oxford nanopore
updated by GenoMax GenoMax • written by Bogdan Bogdan
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 Ming Tommy Tang
0 votes
0 replies
619 views
How to determine which pangenome nodes correspond to hg38 coordinates?
pangenome reference-genome hg38 genomics
written by a5864557 • a5864557
0 votes
0 replies
507 views
LDhat analysis pipeline
recombination ldhat
written by chaudharyc61 • chaudharyc61
0 votes
7 replies
2.6K views
Parsing error in sam file when converting to bam
samtools bwa fastq bam sam
updated by GenoMax GenoMax • written by emily.coger • emily.coger
4 votes
1 reply
1.6K views
GATK site filtering: when should I use VQSR or hard filtering?
vqsr gatk
updated by alba • alba • written by samuelandjw • samuelandjw
0 votes
1 reply
937 views
Missing `pro_ref` Folder in PICRUSt2 Default Files
github picrust2
updated by Ram Ram • written by ameeraelshinawy • ameeraelshinawy
0 votes
1 reply
1.1K views
How to Display Metadata on IGV Visualizations
integrative-genomics-viewer igv
updated by Ram Ram • written by luminea • luminea
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 Ming Tommy Tang • written by AlexStar • AlexStar
0 votes
2 replies
1.2K views
RNA-seq combined treatment interaction experiment design
rna-seq deseq2
updated by Ram Ram • written by Manko47 • Manko47
0 votes
0 replies
1.2K views
Forum: Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping variants
updated by GenoMax GenoMax • written by Ian Ian
10 votes
11 replies
25K views
CIBERSORT deconvolution advice
cibersort cibersortx deconvolution
updated by Nguyen • Nguyen • written by joker33 • joker33
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 • ecSeq Bioinformatics
0 votes
0 replies
653 views
Sesame Data ExperimentHub and related issues
caching sesame methylation
updated by GenoMax GenoMax • written by jain72744 • jain72744
0 votes
0 replies
749 views
Unable to link peaks to genes for multiomics data
multiome multiomics linkpeaks signac 10x
written by sribas.chowdhury888 • sribas.chowdhury888
0 votes
0 replies
576 views
GWAS for Klebsiella isolates
technical help gwas
written by Bahnie • Bahnie
0 votes
0 replies
638 views
CoCoRV - Which file from gnomAD as control
variants rare wes
written by andrebolerbarros • andrebolerbarros
0 votes
1 reply
1.0K views
SNP/kb in chromosome wise
variant snp calling
updated by Pierre Lindenbaum Pierre Lindenbaum • written by adarsh • adarsh
0 votes
0 replies
436 views
time to event GWAS
signals independent
updated by GenoMax GenoMax • written by JJ • JJ
0 votes
9 replies
2.2K views
single-cell zeros handling, inputation and filtration
zeros single-cell
updated by jared.andrews07 jared.andrews07 • written by frarodmar17 • frarodmar17
0 votes
3 replies
1.8K views
submitting to SRA database
files pod5 sra
updated by ATpoint ATpoint • written by baibhu1234 • baibhu1234
0 votes
3 replies
1.3K views
Flattened TSS enrichment x unique fragments from scATAC experiment
atac
updated by jared.andrews07 jared.andrews07 • written by forestyang • forestyang
0 votes
6 replies
2.0K views
determine softmask regions from FASTA
bed fasta softmask
updated by lieven.sterck lieven.sterck • written by Matteo Ungaro • Matteo Ungaro
0 votes
4 replies
1.7K views
Number of reads supporting a structural variant value in Dragen structural variant calling output
structural vcf variants manta
updated by benformatics benformatics • written by ieie • ieie
0 votes
2 replies
1.3K views
Strategy for mapping rat and human gene symbols from scRNA-seq data - dealing with inconsistent nomenclature
orthologs scrnaseq
updated by ATpoint ATpoint • written by dxj294 • dxj294
0 votes
0 replies
791 views
News: online course: R/Bioconductor for Mass Spectrometry and Proteomics
bioconductor r spectrometry mass proteomics
written by Physalia-courses Physalia-courses
0 votes
5 replies
1.6K views
What is the interpretation of sequence enrichment in whole genome sequencing?
sequencing wgs enrichment
updated by GenoMax GenoMax • written by marongiu.luigi marongiu.luigi
0 votes
9 replies
3.0K views
Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the same as in the bam headers! (targets: 10575 from the bam vs 67331 from the ref)
binning metagenomics metabat2
written by samdegregori • samdegregori
0 votes
0 replies
479 views
Combining expression and mutation data from TCGA
tcga
updated by Bastien Hervé Bastien Hervé • written by Maliha • Maliha
0 votes
1 reply
1.3K views
Annotate .fcs files with gated population classification
facs flow cytometry flowjo
updated by Dylan • Dylan • written by Benni • Benni
0 votes
0 replies
516 views
Converting map & ped files to binary file. Missing info
map ped plink
updated by Ram Ram • written by mulderharko • mulderharko
0 votes
2 replies
2.3K views
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord
maftools
updated by garcesj • garcesj • written by alwayshope • alwayshope
0 votes
3 replies
1.1K views
Is there a way or a tool to compare two hmm DNA profiles?
biotool hmmprofile hmm-hmm
written by abarcajose97 • abarcajose97
1 vote
2 replies
1.5K views
LASSO regression for gene selection and clinical variables
lasso feature classification selection edger
updated by Mensur Dlakic Mensur Dlakic • written by fabian • fabian
0 votes
4 replies
1.6K views
How to Check the Quality of a .fasta File for Sequence Alignment?
sequence-alignment fasta quality-control
updated by colindaven colindaven • written by Dikshya • Dikshya
0 votes
3 replies
1.1K views
Kmerfinder database with bacteria, archea, and eukaryotic data
kmer
updated by lieven.sterck lieven.sterck • written by Mark • Mark
0 votes
5 replies
1.4K views
rna-seq reads not passing fastqc
rna-seq fastqc
written by Luna • Luna
0 votes
6 replies
1.8K views
Is there a proper way to choose bins in barplot
visualization plot bar
written by QX • QX
1 vote
1 reply
916 views
Seeking advice for a machine learning project with RNA-seq data
ml gene_expression machine_learning dge deep_learning
updated by dthorbur dthorbur • written by ymd56731 • ymd56731
0 votes
0 replies
768 views
Search and return transcript types from gene symbols by querying mygene.info or ensembl rest APIs
gene ensembl mygene transcriptomics identification
written by m.musgrove • m.musgrove
0 votes
0 replies
824 views
Questions about genome annotation of non-coding RNA with infernal
ncrna annotation
written by Abieskawa • Abieskawa
0 votes
1 reply
874 views
samtools tview special character
samtools bam rna
updated by Pierre Lindenbaum Pierre Lindenbaum • written by from the mountains from the mountains
0 votes
3 replies
1.5K views
snpEff 'java.lang.OutOfMemoryError: Java heap space' problem despite increasing initial and maximum heap size to 10g and 20g respectively
heapsize conda snpeff anaconda java
updated by Alex • Alex • written by millielam • millielam
0 votes
6 replies
1.5K views
Convert miRNA_ID to GENE-symbol
gene_symbol
updated by i.sudbery i.sudbery • written by sorour.hasani • sorour.hasani
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