426 Open source projects that are alternatives of or similar to SemiBin

GraphBin: Refined binning of metagenomic contigs using assembly graphs

🎯 Human transcription factor target genes.

Per-base per-nucleotide depth analysis

Ploidy agnostic phasing pipeline and algorithm

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

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

Genomics data visualization in Python by using matplotlib.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

API for linked biological knowledge

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Project metadata manager for PEPs in Python

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

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

A Kotlin DSL and library to create and plot RNA 2D structures

Assembling the cause of phenotypes and genotypes from NGS data

Open source Java library for computational proteomics

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Stacked Denoising AutoEncoder based on TensorFlow

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

GWAS summary statistics files QC tool

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

exploratory and interactive microbiome analyses based on heatmaps

Classify sequencing reads using MinHash.

Rapid determination of appropriate reference genomes.

Single Cell Analysis Pipelines

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

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

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

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

Compare different differential abundance and expression methods

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

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

Genomics using open source tools, running on GCP or AWS

R package for microbiome biomarker discovery

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

Bystro genetic analysis (annotation, filtering, statistics)

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

React rerelease of MSAViewer

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

A Python platform for Structural Bioinformatics

A faster lmm for GWAS. Supports GPU backend.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

A simple command-line tool to download data from Joint Genome Institute databases

Mulled - Automatized Containerized Software Repository

AMBER: Assessment of Metagenome BinnERs

Genotyping of segregating mobile elements insertions

Predict AMPs in (meta)genomes and peptides

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

Deep learning for Metagenome Assembly Error Detection

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…

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

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

A fast 23andMe genome text file parser, now superseded by arv

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Examples using Clustergrammer2 to explore high-dimensional datasets.

Introduction to the Unix Shell for biologists

Read DNA sequences from colourful Microsoft Word documents