Limnology (Freshwater Science)

BCFtools — comprehensive toolkit for manipulating variant calls in VCF and BCF format. Provides variant calling (mpileup + call), filtering, querying, merging, concatenation, normalization, annotation

1 shared topic • 2 shared operations

BioNumPy — NumPy-based Python library for array-oriented genomics analysis.

1 shared topic • 2 shared operations

Use when performing GWAS fine-mapping with PAINTOR (Probabilistic Annotation INTegratOR). Computes posterior inclusion probabilities (PIPs) for causal variants by integrating summary statistics (Z-sco

1 shared topic • 2 shared operations

Use when working with PolyFun — functionally-informed polygenic fine-mapping from GWAS summary statistics. Computes per-SNP heritability priors using S-LDSC with functional annotations, then runs SuSi

1 shared topic • 2 shared operations

Use when working with SparsePro for GWAS fine-mapping and causal variant identification. Sparse variational inference framework that computes posterior inclusion probabilities (PIPs) and credible sets

1 shared topic • 2 shared operations