651 Open source projects that are alternatives of or similar to graphsim

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Resource of human chromosome schematics & images

A fast whole-genome aligner based on de Bruijn graphs

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

A modular annotation tool for genomic variants

Forward-time simulation in Python using fwdpp

Ultrafast sequence typing and gene detection from NGS raw reads

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

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

A tool to plot significant regions of GWAS

A curated list of awesome bioinformatics software.

GARDENIA: Graph Analytics Repository for Designing Efficient Next-generation Accelerators

A Shared Memory Multithreaded Graph Benchmark Suite for Multicores

Genome-wide imputation pipeline

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Manhattan plot Generator

Transcripts annotation and GO enrichment Fisher tests

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Numerical Encoding for Human Genetic Variants

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Bioconductor package for management of multi-assay data

Keras implementation of Neural Graph Fingerprints as proposed by Duvenaud et al., 2015

Simulation and visualization of articulated rigid body systems in Julia

Nextflow basic tutorial for newbie users

fCoSE: a fast Compound Spring Embedder

Spark VCF data source implementation for Dataframes

Big Compute Learning Labs

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

A collection of ML related stuff including notebooks, codes and a curated list of various useful resources such as books and softwares. Almost everything mentioned here is free (as speech not free food) or open-source.

An easy to use GraphQL API to query country-related data for free and without restrictions

Library for functional graph & geometry algorithms

A simple benchmark system for compiled and interpreted languages.

Identify phage regions in bacterial genomes for masking purposes

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Python-based UCSC genome browser snapshot-taker and gallery-maker

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Multi-robot Exploration Testbed

A library for quantum characterization, verification, validation (QCVV), and benchmarking using pyQuil.

No description or website provided.

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Differential Gene Correlation Analysis

Applications using Parallel Graph AnalytiX (PGX) from Oracle Labs

A suite of tools for benchmarking (load testing) web servers and databases

🐳 Bio-dockers: dockerized bioinformatic tools

Collection of abstract data structures implemented in Java

A library for manipulating bioinformatics sequencing formats in Apache Spark

WebAssembly modules for genomics

Improve the quality of a denovo assembly by scaffolding and gap filling

Use Unity to generate synthetic images for deep learning image segmentation in PyTorch and fastai

GREIN : GEO RNA-seq Experiments Interactive Navigator

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Statistical inference on machine learning or general non-parametric models

Explore rearrangements and copy-number amplifications in a cancer genome

Raspberry Pi benchmarking scripts featuring a storage benchmark with score

Install dependency graphs of Kubernetes Helm Charts

Data Structure and Algorithm for Graphs

Multilocus sequence typing by blast using the schemes from PubMLST

No description or website provided.