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133 search results found

Cs Video Courses ⭐ 62,887

List of Computer Science courses with video lectures.

Awesome Deepbio ⭐ 1,467

A curated list of awesome deep learning applications in the field of computational biology

Graphein ⭐ 932

Protein Graph Library

Scikit Bio ⭐ 833

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Biopandas ⭐ 673

Working with molecular structures in pandas DataFrames

A high-performance, Pythonic language for bioinformatics

A Go package for engineering organisms.

Dash Cytoscape ⭐ 555

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Cobrapy ⭐ 414

COBRApy is a package for constraint-based modeling of metabolic networks.

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Deep Rules ⭐ 198

Ten Quick Tips for Deep Learning in Biology

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

UCSC Genome Browser source tree. Stable branch: "beta".

Biosyntax ⭐ 184

Syntax highlighting for computational biology

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Dna2vec ⭐ 103

dna2vec: Consistent vector representations of variable-length k-mers

Python_biologist ⭐ 101

Python Programming for Biologists

Race and ethnicity Imputation from Disease history with Deep LEarning

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

An R Package for Geneset Enrichment Workflows

Guideline For Computational Biology And Bioinformatics ⭐ 60

The MPI Bioinformatics Toolkit

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

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

Glycowork ⭐ 46

Package for processing and analyzing glycans and their role in biology.

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

A library to build and execute typed scientific workflows

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

A D library for computational biology and bioinformatics

Список вакансий в Департаменте Вычислительной Биологии в компании BIOCAD

Natural language processing of Gene Expression Omnibus data

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

10x Genomics Reads Simulator

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Python implementation of Spatial Analysis of Functional Enrichment (SAFE)

Pycontact ⭐ 34

Analysis of non-covalent interactions in MD trajectories

Contact_map ⭐ 31

Contact map analysis for biomolecules; based on MDTraj

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

Interpretable genotype-phenotype landscape modeling

Python API for the Interactive Tree of Life (iTOL)

Compbioftw ⭐ 30

Essential introductory materials to get into computational biology.

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (EMNLP 2023)

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Biosymbols.jl ⭐ 28

Nucleic and amino acid primitive types

Workflows ⭐ 28

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Soapdenovo Trans ⭐ 27

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

Straindesign ⭐ 27

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

Causalpath ⭐ 27

A project for exploring differentially active signaling paths related to proteomics datasets

Create WDL documentation using Markdown.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Soap3 Dp ⭐ 24

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

Teaching ⭐ 24

Code and files used in teaching and training courses.

🌎 Review materials for bioinformatics, computational biology, and science in general

Fastheatmap ⭐ 23

Super high performance interactive heatmap software

The Microbiome Interpretable Temporal Rule Engine

Data visualization library for creating interactive graphs and dashboards for bioinformatics etc.

Smart search engine for all bioinformatics databases worldwide

Teaching ⭐ 20

Courses & workshops led by members of the Krishnan Lab.

Aptasuite ⭐ 20

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Team Rosalind Project ⭐ 18

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Slamdunk ⭐ 18

Streamlining SLAM-seq analysis with ultra-high sensitivity

Screenlamp ⭐ 18

screenlamp is a Python toolkit for hypothesis-driven virtual screening

Biosemble ⭐ 17

AI assembly of bioNLP wordnets

Bioinformatics ⭐ 17

Course materials for Computational Biology and Bioinformatics - BI462

Bio Phylo ⭐ 15

Bio::Phylo - Phyloinformatic analysis using Perl

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Brendapyrser ⭐ 14

A Python parser for the BRENDA database

DeepSEA in TensorFlow

Sars Cov 2_b.1.1.529_spike Rbd_predictions ⭐ 14

AlphaFold2 and RoseTTAFold predictions of the SARS-CoV-2 B.1.1.529 variant Spike protein with HADDOCK antibody interactions

Hypothesis Bio ⭐ 14

Hypothesis extension for computational biology

Query sequence database by HMMs arranged in predefined synteny structure

Bioinformatics Conf Vids ⭐ 13

List of conferences with talk videos posted online

Toolchest Client Python ⭐ 13

Toolchest Python client

Phylotoast ⭐ 12

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Ammolite ⭐ 12

Visualize structure data from Biotite with PyMOL

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

Compbio Gists ⭐ 12

Computational Biology & Bioinformatics Resources

Epidemic ⭐ 11

EPIDEMIC is an easy-to-run educational toolkit for epidemiological analysis.

Isambard ⭐ 11

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

iCodon customizes gene expression based on the codon composition

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Pgp_reconstruction ⭐ 10

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Autopacmen ⭐ 10

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

Guidescan Cli ⭐ 10

A gRNA database generation tool.

A bare metal Python library for building and manipulating protein molecular structures

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

Randomwalkrestartmh ⭐ 10

A package to perform Random Walk with Restart on different types of networks

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