41 projects
pankmer
Generate a PanGenome given a set of genomes
pygna2
Geneset Network Analysis
loreme
Extract Methylation calls from ONT or PB long read data
gtracks
Plot genome track data
pysmoove-summary
Summarize pysmoove SV calling VCF results in a BED-like format
mutil
Utility for managing memory with cgroup
phased-methylation
Pipeline for phased methylation calling on raw nanopore data
gff2bed
Convert GFF3-formatted data to BED format
seqalign
Manage sequence alignments
pyQuASAR-genotype
Command line tool for genotyping with QuASAR
pyQuASAR
Wrap quasar for pipelines
pyhg19
Utilities for working with human genome build hg19
pydbsnp
Interface with dbSNP VCF data
py1kgp
Utilities for working with 1000 Genomes data
pileups
Manipulate files of the pileup format from SAMtools
picardtools
python3 interface with Picard Tools from Broad institute
overdisp
Estimation of overdispersion parameters
luciferase
Helper functions for luciferase data
funcgenom
Classes and functions for functional genomics analysis
Flask-FTSCursor
An extension to facilitate using FTSCursor with flask
ftscursor
A sqlite3 cursor with extra methods to support FTS3/4/5
finrich
Calculate enrichment of genomic regions with fine-mapping signals
estimateratio
Estimate ratios of random variables
dismotif
disrupted motifs
coloc
the COLOC method by Giambartolomei et al.
chipseqpeaks
Easy management of ChIP-seq peak calling
betabernsum
Sums of beta-bernoulli random variables
bbprop
Hypothesis test for difference of beta-binomial proportions
bbpmf
Probability mass function for a beta-binomial distribution
allelicimbalance
Utilities for studying allelic imbalance
tssenrich
Calculate TSS enrichment for ATAC-seq data
wasp-map
Utilites for the mapping pipeline from WASP
accelasc
implementation of accel_asc algorithm for integer partitions
tempfifo
This module creates temporary named pipes
splitbam
Split a BAM file into two subsamples
sumstats
utilities for working with GWAS summary statistics
specivar
Filter VCF to variants that are specific to a sample group
pysmoove
Execute the population-level SV calling workflow for smoove
acdumo
Accelerated dual momentum
ldsc2
Simplify stratified LD score regression
jsontab
Agnostically load JSON or tabular data
