328 Open source projects that are alternatives of or similar to shiny-iatlas

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

Provide R access to the NCI Genomic Data Commons portal.

A basic framework for pulmonary nodule detection and characterization in CT

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.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

An R framework for phylostratigraphy

Cancer-dedicated gene set interpretation

Resource of human chromosome schematics & images

My collection of light bioinformatics analysis pipelines for specific tasks

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

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

A web application to visualize and edit pathway models

Grammar of Scalable Linked Interactive Nucleotide Graphics

Text mining cancer biomarkers for the CIVIC database

Tools for analyzing 10X Genomics data

A faster lmm for GWAS. Supports GPU backend.

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.

A proof of concept of RNAseq pipeline

A fast, scalable, and accurate local ancestry method.

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

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

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

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

A modular annotation tool for genomic variants

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

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Interactive assembly and analysis of RAD-seq data sets

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

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

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

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

Cancer Predisposition Sequencing Reporter (CPSR)

Clustering scRNAseq by genotypes

Predict AMPs in (meta)genomes and peptides

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

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

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

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

PERF is an Exhaustive Repeat Finder

A tool to plot significant regions of GWAS

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

Workshop in omics integration and systems biology

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

Gene fusion detection and visualization

Learn interpretable computational phenotyping models from k-merized genomic data

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Precision HLA typing from next-generation sequencing data

Command line utility for manipulating Illumina-generated FastQ files.

mgatk: mitochondrial genome analysis toolkit

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Environmental DNA metabarcoding taxonomic identification

Multilocus sequence typing by blast using the schemes from PubMLST

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

3D hotspot mutation proximity analysis tool

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

Toolkit for preparing genomes for submission to NCBI