416 Open source projects that are alternatives of or similar to echolocatoR

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

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

Simple pure Python SAM parser and objects for working with SAM records

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

exploratory and interactive microbiome analyses based on heatmaps

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Unsupervised domain adaptation method for relation extraction

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

3D printed sculpture of a DNA molecule, showing my own genome

Improving genome bins through the combination of different binning programs

Mapping-Assisted Targeted-Assembly for Metagenomics

📊 Codon usage tables in code-friendly format + Python bindings

Bystro genetic analysis (annotation, filtering, statistics)

Classify sequencing reads using MinHash.

Per-base per-nucleotide depth analysis

Single Cell Analysis Pipelines

A Python platform for Structural Bioinformatics

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Find causal cell-types underlying complex trait genetics

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Mulled - Automatized Containerized Software Repository

A permissively licensed library designed to replace Illumina's Experiment Manager

Genomics data visualization in Python by using matplotlib.

Genomics using open source tools, running on GCP or AWS

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Introduction to the Unix Shell for biologists

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

MView extracts and reformats the results of a sequence database search or multiple alignment.

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Core BioPerl 1.x code

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

A curated list of resources for machine learning for small-molecule drug discovery

A modular annotation tool for genomic variants

React rerelease of MSAViewer

Perform GWAS using the FarmCPU model.

Heritability, genetic correlation and functional enrichment estimation for case-control studies

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Assembling the cause of phenotypes and genotypes from NGS data

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.

A package for designing compact and comprehensive capture probe sets.

Structural variation caller using third generation sequencing

Stacked Denoising AutoEncoder based on TensorFlow

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

JavaScript VisualizationTools

Genotyping of segregating mobile elements insertions

Read and write FASTQ and FASTA efficiently from Python

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

A library to build and execute typed scientific workflows

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

My own tools code for NGS data analysis (Next Generation Sequencing)