300 Open source projects that are alternatives of or similar to smartas

Provide R access to the NCI Genomic Data Commons portal.

Bioconductor package for management of multi-assay data

Interactive R package to quantify, analyse and visualise alternative splicing

TCGA data acquisition and processing for Project Cognoma

An interactive web portal for exploring immuno-oncology data

Clustering scRNAseq by genotypes

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

List of IARC bioinformatics nextflow pipelines

A Python-Tensorflow neural network for classifying cancer data

PERF is an Exhaustive Repeat Finder

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

Fast hash function for DNA sequences

Learn interpretable computational phenotyping models from k-merized genomic data

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Grammar of Scalable Linked Interactive Nucleotide Graphics

(WIP) best-practices workflow for rare disease

A package for designing activity-informed nucleic acid diagnostics for viruses.

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

Cancer Predisposition Sequencing Reporter (CPSR)

Predict AMPs in (meta)genomes and peptides

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

Chanjo provides a better way to analyze coverage data in clinical sequencing.

find large indels (in the blind spot between GATK/freebayes and SV callers)

Text mining cancer biomarkers for the CIVIC database

3D hotspot mutation proximity analysis tool

Cancer-dedicated gene set interpretation

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

A proof of concept of RNAseq pipeline

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

Compute N50/NG50 and auN/auNG

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

mgatk: mitochondrial genome analysis toolkit

echt rapid variant annotation and filtering

Interactive assembly and analysis of RAD-seq data sets

Toolkit for preparing genomes for submission to NCBI

An R framework for phylostratigraphy

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

Tools for analyzing 10X Genomics data

A faster lmm for GWAS. Supports GPU backend.

A basic framework for pulmonary nodule detection and characterization in CT

Data Wrangling and Processing for Genomics

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

My collection of light bioinformatics analysis pipelines for specific tasks

Resource of human chromosome schematics & images

A package for designing compact and comprehensive capture probe sets.

A modular annotation tool for genomic variants

A fast, scalable, and accurate local ancestry method.

A tool to plot significant regions of GWAS

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

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

Environmental DNA metabarcoding taxonomic identification

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

Version 2.1.0 released

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

Complex structural variant detection from WGS data