330 Open source projects that are alternatives of or similar to bap

mgatk: mitochondrial genome analysis toolkit

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Multiome GRN inference.

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

CUT&RUN and CUT&Tag data processing and analysis

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Inference of switch-like differential expression along single-cell trajectories

Single cell analysis in the browser

simple viewer for variant call format using htslib

Collection of scripts for bacterial genomics

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

a pileup library that embraces the huge

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

A secure encryption tool for genomic data

Conditional out-of-distribution prediction

Genome Annotation Without Nightmares

A tool that allows to get UMI counts from a single cell protein assay

Examples to get started with IBM Functional Genomics Platform

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Large genome reassembly based on Hi-C data, continuation of GRAAL

Single-cell copy number calling and event history reconstruction.

High-performance error correction for Illumina resequencing data

The GenePattern Server web application

Easy genetic ancestry predictions in Python

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

ntHash implementation in Rust

Mouse cell atlas

Python package and CLI for whole-genome duplication related analyses

R package to visualize gene expression data based on weighted kernel density estimation

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Finds SNP sites from a multi-FASTA alignment file

Ultrafast sequence typing and gene detection from NGS raw reads

Detecting methylation using signal-level features from Nanopore sequencing reads

GA4GH Variation Representation Python Implementation

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Introduction to the Command Line for Genomics

Biopython Jupyter Notebook tutorial to characterize a small genome

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Phage-Host Interaction Search Tool

Single-Cell Omics Preparation Entity Tools

simuG: a general-purpose genome simulator

use the noise

Genome-wide imputation pipeline

Efficient genotyping bi-allelic SNPs on single cells

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Predicting regulatory DNA elements based on epigenomic signatures

Manhattan plot Generator

Population assignment analysis using R

Tools for single-cell data processing

DriverPower

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Next-Gen Sequencing tools from the Horvath Lab

Convert between AnnData and SingleCellExperiment

Genomics Workflows on AWS

Find target sites for the miRNAs in genomic sequences

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A tool for fast and accurate summarizing of variant calling format (VCF) files