444 Open source projects that are alternatives of or similar to StackedDAE

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

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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.

Read and write FASTQ and FASTA efficiently from Python

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

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

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

🎯 Human transcription factor target genes.

Improving genome bins through the combination of different binning programs

Classify sequencing reads using MinHash.

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

Compute N50/NG50 and auN/auNG

Fast hash function for DNA sequences

Fast and flexible ORF finder

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WebGL Heatmap Viewer for Big Data and Bioinformatics

Open source Java library for computational proteomics

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

Feature extraction algorithm for genomic data

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Method to optimally select samples for validation and resequencing

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Single Cell Analysis Pipelines

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

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

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

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

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

API for linked biological knowledge

Rapid determination of appropriate reference genomes.

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

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

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

Bystro genetic analysis (annotation, filtering, statistics)

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

Manuscript for functional prediction of transcriptomic “dark matter” across species

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

GWAS summary statistics files QC tool

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

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

A Python platform for Structural Bioinformatics

An R package for reproducible and automated ADMIXTOOLS analyses

A package for designing compact and comprehensive capture probe sets.

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

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

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

GRAph-based Finding of Individual Motif Occurrences

Mulled - Automatized Containerized Software Repository

dysgu-SV is a collection of tools for calling structural variants using short or long reads

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Useful bioinformatic scripts

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

Unsupervised domain adaptation method for relation extraction

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