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0 votes
6 replies
2.2K views
10x Cell Ranger Multi
10x single cell multiplexing
updated by Kevin Blighe 9.0K • | written by zizigolu 438
0 votes
4 replies
1.9K views
Critique or Feedback of filtering strategy for LIANA+ results using spatially informed bivariate metrics
liana spatial-transcriptomics visiumhd
written by danielpintard 2
0 votes
20 replies
10K views
PacBio raw data trimming and cleaning
pacbio trimming cleaning qc
updated by lieven.sterck 1.6K • | written by misterie 11
0 votes
0 replies
967 views
News: Online Course - A Practical Introduction to NGS Data Analysis (December 3-5, 2025) - 32% Off
variantcalling illumina workshop dna-seq rna-seq
written by ecSeq Bioinformatics 9
0 votes
10 replies
2.2K views
Count unique fragments from a given BAM file
dna bam
updated by GenoMax 16K • | written by Ankit 52
0 votes
2 replies
3.0K views
Merlin ped file issue
linkage merlin
updated by bcvona 0 • | written by emyli 1
0 votes
2 replies
9.6K views
GO Terms significance Scoring
go semantic annotation
updated by geneontologyhelp 57 • | written by Marek 0
1 vote
2 replies
1.2K views
Ribo-seq Trimming Issue: Massive Read Loss in Paired-end Mode
trimming paired-end riboseq
updated by stuart archer 18 • | written by Sammy 1
0 votes
1 reply
615 views
Running snpEff with hg19 reference genome (config file question)
snpeff hg19
updated by Pierre Lindenbaum 17K • | written by shpak.max 8
0 votes
3 replies
1.8K views
Error when opening CEL files in python
python
updated by richard.may0810 0 • | written by Paula 0
0 votes
2 replies
1.2K views
NAT Vs T samples DA analysis
abundance differential microbiome
updated by Kevin Blighe 9.0K • | written by San 0
0 votes
1 reply
1.6K views
problem with reading cel files from [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [HuGene20stv1_Hs_ENTREZG_17.0.0]
normalization microarray
updated by Kevin Blighe 9.0K • | written by drwaqasakbar 0
0 votes
0 replies
837 views
How to select background metabolite sets for differential metabolite enrichment analysis?
enrichment ora
updated by Kevin Blighe 9.0K • | written by Edward 0
0 votes
1 reply
967 views
How much coverage is needed for high-quality phylogenetic and admixture analyses using short-read WGS in plants?
coverage
updated by Kevin Blighe 9.0K • | written by rosaceae 0
0 votes
2 replies
1.3K views
Does the weights file stay the same for a different model organism
machine-learning
updated by Kevin Blighe 9.0K • | written by Sharma 0
0 votes
4 replies
6.5K views
SNP calling with bacterial assembled genome
variant-calling snp bacteria
updated by Kevin Blighe 9.0K • | written by yesquokkan 1
0 votes
1 reply
1.1K views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
plm mapping llm extraction relation
updated by Kevin Blighe 9.0K • | written by DEPANSHI 0
0 votes
1 reply
881 views
Small Molecule Databases and clustering
polyethylene moleculardatabase molecule pet trephthalate
updated by Kevin Blighe 9.0K • | written by yarrowmadrona 1
0 votes
2 replies
1.2K views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
data transcriptomic
updated by Kevin Blighe 9.0K • | written by olusolaxx 0
0 votes
2 replies
1.6K views
Clustal omega on M1 Mac
alignment clustal-omega macos
updated by Kevin Blighe 9.0K • | written by kate-nelis 0
0 votes
2 replies
1.6K views
Depth and genotype quality in vcf file
vcf depth wes variants
updated by Kevin Blighe 9.0K • | written by ashaneev07 5
0 votes
5 replies
2.4K views
Need help with fgsea
scrnaseq fgsea
updated by Kevin Blighe 9.0K • | written by bio_info 2
0 votes
3 replies
1.5K views
RNA-seq data compared to qRT-PCR
rna-seq
updated by Kevin Blighe 9.0K • | written by SeoG 1
0 votes
3 replies
2.1K views
biomart hangs
biomart
updated by Kevin Blighe 9.0K • | written by ramiro.barrantes 6
0 votes
7 replies
2.0K views
PCA interpretation
rnaseq pca
updated by Kevin Blighe 9.0K • | written by nuriagaralon 2
1 vote
28 replies
9.0K views
Did anyone manage to successfully run HLAScan and get results?
hla-typing ngs
updated by Kevin Blighe 9.0K • | written by zeynep 1
0 votes
30 replies
5.2K views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method r
updated by Kevin Blighe 9.0K • | written by Chaimaa 26
0 votes
44 replies
10K views
Annotation of huge number of CNV files
cnv annotation tcga
updated by Kevin Blighe 9.0K • | written by nazaninhoseinkhan 53
0 votes
46 replies
11K views
SAM file wrong? help with validatesamfile
exome
updated by Kevin Blighe 9.0K • | written by cristina_sabiers 11
3 votes
39 replies
21K views
Differential gene Analysis by Limma
limma microarray r
updated by Kevin Blighe 9.0K • | written by Mo 92
1 vote
56 replies
18K views
hash function for DNA sequences
hash hashing dna
updated by Kevin Blighe 9.0K • | written by midox 29
1 vote
4 replies
26K views
Subsetting - Raw Counts from Seurat Object
seurat raw counts rna-seq
updated by Kevin Blighe 9.0K • | written by David_emir 50
1 vote
7 replies
38K views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
updated by Kevin Blighe 9.0K • | written by star 36
0 votes
14 replies
42K views
[main_samview] fail to read the header from sample.bam
alignment
updated by Kevin Blighe 9.0K • | written by sambioinfo2018 2
8 votes
23 replies
64K views
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking for family relationships a priori?
plink vcf fam gatk vcftools
updated by Kevin Blighe 9.0K • | written by gaelgarcia 28
0 votes
1 reply
988 views
TOM matrix WGCNA
wgcna
updated by Kevin Blighe 9.0K • | written by frarodmar17 4
0 votes
1 reply
2.0K views
Two-sample Mendelian Randomization (MR) summary statistics
gwas randomization mendelian
updated by Kevin Blighe 9.0K • | written by handecadir 0
0 votes
1 reply
1.6K views
Error, 'object too long to compress'
orthologs oma oma
updated by Kevin Blighe 9.0K • | written by felix_langschied 0
0 votes
1 reply
841 views
KEGG Orthologs (KO) from 16S vs. Metabolites
picrust2 microbiome metabolome
updated by andres.firrincieli 412 • | written by Arunabh Sharma 1
0 votes
1 reply
870 views
Direct RNA-seq Nanopore
drna
updated by Kevin Blighe 9.0K • | written by frarodmar17 4
0 votes
5 replies
7.2K views
cellranger mkref fail/error
mkref multiple_species customtranscriptome cellranger transcriptome
updated by Kevin Blighe 9.0K • | written by tatsispolychronis 2
0 votes
2 replies
1.5K views
Using soupX on single nucleus RNA seq data
rnaseq soupx singlenucleus snrnaseq
updated by Kevin Blighe 9.0K • | written by happymuffin24 0
0 votes
2 replies
6.1K views
TOPMed Imputation - More than 10000 allele switches
imputation topmed
updated by Kevin Blighe 9.0K • | written by Akshaj 0
0 votes
2 replies
5.6K views
Question regarding batch effect in TCGA-HNSC
cancer deseq2 sva tcga
updated by Kevin Blighe 9.0K • | written by Hamada 0
0 votes
0 replies
510 views
BLAST database error while using HiFiAdapterfilt to filter out adapter contaminants from PacBio raw reads
blast pacbio ncbi assembly genome
updated by Kevin Blighe 9.0K • | written by pranavdatar01 1
0 votes
0 replies
6.5K views
rsid in full data table for GSA array but not in the final vcf file
array gsa
updated by Kevin Blighe 9.0K • | written by 1769mkc 127
0 votes
0 replies
6.0K views
Radial plot help
radial-plots bulls-eye
updated by Kevin Blighe 9.0K • | written by bioinformatics_rk 1
0 votes
3 replies
4.1K views
Forum: Looking for Entry-Level Bioinformatics Project Ideas to Build My Portfolio
bioinformatics genomics next-generation-sequencing
updated by Ram 4.5K • | written by Samudraneel 1
0 votes
1 reply
900 views
Is there a difference between signalValue and FoldEnrichment in peak files obtained by MACS2 peakcalling
chip-seq cutandrun
updated by rfran010 174 • | written by sribas.chowdhury888 0
0 votes
3 replies
1.8K views
ATAC-SEQ FRAGMENT SIZE
size fragment picard atac-seq
updated by ATpoint 9.1K • | written by Irene 1
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