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

Adjacency-constrained hierarchical clustering of a similarity matrix

A faster lmm for GWAS. Supports GPU backend.

📊 Identify cell types and pathways affected by genetic risk loci.

Mixed models @lme4 + custom covariances + parameter constraints

GWAS summary statistics files QC tool

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

Fast alignment and preprocessing of chromatin profiles

Fast and flexible ORF finder

Method to optimally select samples for validation and resequencing

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

A computational library for learning and evaluating biological knowledge graph embeddings

Compute N50/NG50 and auN/auNG

An open-access bioinformatics text

Read DNA sequences from colourful Microsoft Word documents

Python API for comprehensive GWAS analysis using GEMMA

Fast motif matching in R

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

WebGL Heatmap Viewer for Big Data and Bioinformatics

Version 5 of the CAFE phylogenetics software

A curated list of awesome bioinformatics software.

Provide R access to the NCI Genomic Data Commons portal.

Feature extraction algorithm for genomic data

Rapid determination of appropriate reference genomes.

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

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

exploratory and interactive microbiome analyses based on heatmaps

Unsupervised domain adaptation method for relation extraction

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

Mapping-Assisted Targeted-Assembly for Metagenomics

Bystro genetic analysis (annotation, filtering, statistics)

Per-base per-nucleotide depth analysis

A Python platform for Structural Bioinformatics

Find causal cell-types underlying complex trait genetics

Mulled - Automatized Containerized Software Repository

Genomics data visualization in Python by using matplotlib.

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

Introduction to the Unix Shell for biologists

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

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

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

React rerelease of MSAViewer

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

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.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

A package for designing compact and comprehensive capture probe sets.

Stacked Denoising AutoEncoder based on TensorFlow

🎯 Human transcription factor target genes.

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Genotyping of segregating mobile elements insertions

Useful bioinformatic scripts

Ploidy agnostic phasing pipeline and algorithm

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…