529 Open source projects that are alternatives of or similar to 2020plus

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…

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Provide R access to the NCI Genomic Data Commons portal.

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

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

De novo assembly based variant calling pipeline for Illumina short reads

A D library for computational biology and bioinformatics

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

The Microbiome Interpretable Temporal Rule Engine

Introduction to the Unix Shell for biologists

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

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

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Generative Forests in Python

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

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

BACNET is a Java based platform to develop website for multi-omics analysis

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

Mapping-Assisted Targeted-Assembly for Metagenomics

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

A simplified pipeline for ctDNA sequencing data analysis

exploratory and interactive microbiome analyses based on heatmaps

Build and maintain multiple custom conda environments all in once place.

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

A curated list of awesome bioinformatics software.

Web client for CIViC: Clinical Interpretations of Variants in Cancer

The Ontology for Biomedical Investigations

Multi-task deep learning framework for multi-omics data analysis

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

Project metadata manager for PEPs in Python

micca - MICrobial Community Analysis

Predict plasmids from uncorrected long read data

Sample search by metadata and features

Examples using Clustergrammer2 to explore high-dimensional datasets.

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

VirNet: A deep attention model for viral reads identification

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Federated Learning based Deep Learning. Docs: https://fets-ai.github.io/Front-End/

Earl Grey: A fully automated TE curation and annotation pipeline

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

No description or website provided.

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

DOM Text Based Multiple Sequence Alignment Library

A library to build and execute typed scientific workflows

Curated list of bioinformatics formats and publications

Fast motif matching in R

A python library to build Model Trees with Linear Models at the leaves.

React rerelease of MSAViewer

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Genotyping of segregating mobile elements insertions

MMseqs2 app to run on your workstation or servers

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

No description or website provided.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

The uncompromising Snakemake code formatter

WebLogo 3: Sequence Logos redrawn

Phylogenetic trees in Julia