339 Open source projects that are alternatives of or similar to switchde

mgatk: mitochondrial genome analysis toolkit

Transcripts annotation and GO enrichment Fisher tests

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

CUT&RUN and CUT&Tag data processing and analysis

Fast visualization tool for large-scale and high dimensional single-cell data

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Bead-based single-cell atac processing

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

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

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

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

Genetic Map Comparison

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

echt rapid variant annotation and filtering

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.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Bystro genetic analysis (annotation, filtering, statistics)

No description or website provided.

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

Version 2.1.0 released

PERF is an Exhaustive Repeat Finder

spatial transcriptome, single cell

Introduction to Cloud Computing for Genomics

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Interactive R package to quantify, analyse and visualise alternative splicing

Complex structural variant detection from WGS data

Make rapid visualizations of RNA-seq data in R

Fast hash function for DNA sequences

Fast alignment and preprocessing of chromatin profiles

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

Feature Annotation Location Description Ontology

Data Wrangling and Processing for Genomics

An ontology of cell types

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

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

An interactive web portal for exploring immuno-oncology data

Assembling the cause of phenotypes and genotypes from NGS data

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

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

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

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

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

Compute N50/NG50 and auN/auNG

Provide R access to the NCI Genomic Data Commons portal.

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Toolkit for preparing genomes for submission to NCBI

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

(WIP) best-practices workflow for rare disease

A faster lmm for GWAS. Supports GPU backend.

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

A curated list of awesome bioinformatics software.

Reference mapping for single-cell genomics

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

My collection of light bioinformatics analysis pipelines for specific tasks

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

Papers with code for single cell related papers

A modular annotation tool for genomic variants

Environmental DNA metabarcoding taxonomic identification

An open-access bioinformatics text