Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: rare-disease

Repositories

neurogenomics/rare_disease_celltyping

Code, data and results associated with the "Rare diseases cell-typing" project.

Language: HTML - Size: 499 MB - Last synced: about 8 hours ago - Pushed: 24 days ago - Stars: 6 - Forks: 0

gagneurlab/FRASER-analysis

Accompanying analysis code for the FRASER manuscript

Language: R - Size: 4.67 MB - Last synced: about 17 hours ago - Pushed: over 3 years ago - Stars: 23 - Forks: 7

bschilder/thesis

PhD thesis written in Quarto.

Language: HTML - Size: 605 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

monarch-initiative/SvAnna

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Language: Java - Size: 3.72 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 29 - Forks: 4

neurogenomics/MSTExplorer

Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.

Language: R - Size: 5.6 MB - Last synced: about 8 hours ago - Pushed: 4 days ago - Stars: 1 - Forks: 1

hms-dbmi/RaMeDiES

Statistical models for finding de novo recurrence and compound heterozygosity across rare disease patient cohorts

Language: Python - Size: 113 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 2 - Forks: 0

IdeRare Phenotype Analysis suite : Convert Indonesia SATUSEHAT terminology (SNOMED-CT, LOINC, ICD-10) to Rare Disease Terminology / Ontology (HPO, OMIM) and find the likelihood differential gene and disease explaining patient phenotype

Language: Jupyter Notebook - Size: 15.1 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

ivanwilliammd/IDeRare

Indonesia Exome Rare Disease Variant Discovery Pipeline. Phenotype analysis part available on Streamlit and PyPi

Language: Jupyter Notebook - Size: 42.3 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

c-mertes/FRASER

FRASER - Find RAre Splicing Events in RNA-seq

Language: R - Size: 14.6 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 30 - Forks: 19

cluhaowie/VizCNV

VizCNV is an interactive tool designed to analyze and visualize CNVs from short read WGS data in rare disease research. Built on R Studio Shiny, it streamlines the identification of complex genomic rearrangements and facilitates advancements in understanding and diagnosing rare genetic conditions.

Language: R - Size: 125 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 2

ZhuChaoY/RDKG-115

RDKG-115: Assisting Drug Repurposing and Discovery for Rare Diseases by Trimodal Knowledge Graph Embedding

Language: Python - Size: 256 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 2 - Forks: 0

nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 11.1 MB - Last synced: about 16 hours ago - Pushed: about 17 hours ago - Stars: 72 - Forks: 33

4pygmalion/ASC3

3ASC: Novel Variant prioritization system for Jointly prioritizing SNV and CNV and classifying reportability in rare disease

Language: Jupyter Notebook - Size: 2.29 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 4 - Forks: 0

neurogenomics/HPOExplorer

Functions for working with the Human Phenotype Ontology data

Language: R - Size: 10.9 MB - Last synced: about 8 hours ago - Pushed: 20 days ago - Stars: 2 - Forks: 1

brentp/slivar

genetic variant expressions, annotation, and filtering for great good.

Language: Nim - Size: 3.25 MB - Last synced: 8 days ago - Pushed: 5 months ago - Stars: 240 - Forks: 21

NCBI-Hackathons/UPWARD

UPWARD: Uniting People Working Against Rare Diseases

Language: PHP - Size: 16.5 MB - Last synced: 24 days ago - Pushed: almost 5 years ago - Stars: 6 - Forks: 1

mims-harvard/SHEPHERD

SHEPHERD: Deep learning for diagnosing patients with rare genetic diseases

Language: HTML - Size: 638 KB - Last synced: 12 days ago - Pushed: 11 months ago - Stars: 35 - Forks: 6

jt-nti/rare-disease-day-addisons

Addison's Disease presentation for Rare Disease Day 2023

Size: 6.78 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

kbellonpizarro/Harvard-Rare-Disease-Hackathon-2024

Repo of the 2024 Harvard Rare Disease Hackathon projects.

Size: 103 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1

PabloBotas/LayRareDiseases

Repository to develop layperson descriptions of rare diseases

Language: Python - Size: 2.88 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

uab-cgds-worthey/DITTO-UI

Easy to use web interface for biologists to look for genetic variants and understand their deleteriousness using DITTO scores.

Language: Python - Size: 2.22 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

Oshlack/MINTIE

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

Language: Python - Size: 21.8 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 32 - Forks: 7

brentp/rare-disease-wf

(WIP) best-practices workflow for rare disease

Language: Nextflow - Size: 548 KB - Last synced: 8 days ago - Pushed: about 1 year ago - Stars: 56 - Forks: 8

open-prophetdb/biomedgps-data

Biomedical knowledge graph & graph neural network models for drug repurposing.

Language: Jupyter Notebook - Size: 105 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

molgenis/molgenis-rdconnect-report

A program to generate the summary statistics for the RD-Connect Sample Catalogue.

Language: Swift - Size: 40 KB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

neurogenomics/RareDiseasePrioritisation

Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.

Language: HTML - Size: 77.9 MB - Last synced: about 8 hours ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

halbritter-lab/pld-progression-grouper

PLD-Progression Grouper - visualize and analyze the progression of Polycystic Liver Disease (PLD) through user-inputted clinical data

Language: Vue - Size: 5.32 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

scholl-lab/vcf-filtering

A collection of scripts for filtering annotated variant call format files

Language: Shell - Size: 101 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

foundation29org/RareCrowds

Package to serve public and freely-available data from rare disease patients.

Language: Python - Size: 24.6 MB - Last synced: 10 days ago - Pushed: over 2 years ago - Stars: 7 - Forks: 6

cancerbits/shahin2021_ikzf2 📦

Code repository accompanying the paper by Shahin et al. (2021), Sci. Immunol.

Language: R - Size: 17.6 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

julienbrg/med-wave Fork of diffusioncon/MedWave-Ocean-Protocol

Med Wave connects doctors working on the same diseases and enable cooperation between them at a global scale.

Language: JavaScript - Size: 185 KB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

berntpopp/morbidgenes

Monthly updated list of diagnostically relevant genes

Language: R - Size: 169 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

greenelab/brd-net

Transfer learning for uncovering the biology underlying rare disease

Language: Jupyter Notebook - Size: 1.77 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 1

ejp-rd-vp/CDE-semantic-model Fork of LUMC-BioSemantics/ERN-common-data-elements

Semantic data model of the set of common data elements for rare disease registration

Size: 153 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 12 - Forks: 9

Carike/Kawasaki-Disease-ZA

Resource page about Kawasaki Disease and any helpful information we find. The focus will be on South Africa but not limited just the country. We want to create awareness and provide information, in particular to parents.

Size: 3.91 KB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

NajiaAhmadi/VisualisationWithPython

Graphics for the article "Methods used in the development of Common Data Models for health data – a Scoping Review"

Language: Jupyter Notebook - Size: 3.06 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

Language: C++ - Size: 89.8 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 5 - Forks: 0

lasseignelab/230227_JW_Setbp1Manuscript

Framework for investigation of cell-type-specific regulation and expression in rare disease

Language: R - Size: 221 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

petermchale/trfermikit

Discover VNTR-associated DELs that are hard to find using Illumina reads

Language: Jupyter Notebook - Size: 45.8 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

acadTags/Rare-disease-identification

Rare disease identification from free-text clinical notes with ontologies and weak supervision

Language: Python - Size: 4.93 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 21 - Forks: 5

BCM-Lupskilab/VizCNV Fork of cluhaowie/VizCNV

Language: R - Size: 119 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

Related Keywords

rare-disease 55 genomics 9 bioinformatics 6 genetics 5 rare-variant-analysis 5 diagnostics 4 rna-seq 4 knowledge-graph 3 database 3 phenotype-prediction 3 phenotype-ontologies 3 scrna-seq 3 human-phenotype-ontology 3 outlier-detection 3 r 3 drug-repurposing 2 shiny-apps 2 splicing 2 enrichment-analysis 2 kidney-disease 2 clinvar 2 workflow 2 phenotype-genotype-information 2 phenotype-exchange-format 2 structural-variation 2 mendelian-genetics 2 immunology 2 multiomics 2 python 2 patient-data 2 vcf 2 variant-calling 2 open-data 2 ontologies 2 fair-data 2 r-package 2 rna-seq-analysis 2 ontology 2 genomics-analysis 1 single-nuclei-rna-sequencing 1 network-biology 1 translational-research 1 illumina-sequencing 1 sequencing 1 sequence-alignment 1 tandem-repeats 1 whole-exome-sequencing 1 whole-genome-sequencing 1 clinical-notes 1 discharge-summaries 1 entity-linking 1 mimic-iii 1 ontology-matching 1 ordo 1 pipeline 1 genome 1 panel 1 analysis 1 gene-expression 1 methodology 1 tool 1 common-data-elements 1 fair 1 rdf-model 1 rdf-schema 1 kawasaki 1 kawasaki-disease 1 common-data-model 1 data-harmonization 1 data-standards 1 healthcare-datasets 1 literature-review 1 scoping-review 1 cancer-genomics 1 k-mer 1 pan-genome 1 reference-free 1 variant-filtering 1 community-detection 1 modularity 1 multilayer 1 network 1 trajectories 1 genetic 1 recommander-system 1 mitochondrial 1 iih 1 ai 1 ai4good 1 ai4health 1 fhir 1 gene-network 1 neo4j 1 protein-protein-interaction 1 retina 1 gtube 1 input 1 medical 1 ostomy 1 output 1

GitHub topics: rare-disease

cancerbits/shahin2021_ikzf2 📦

julienbrg/med-wave Fork of diffusioncon/MedWave-Ocean-Protocol

ejp-rd-vp/CDE-semantic-model Fork of LUMC-BioSemantics/ERN-common-data-elements

BCM-Lupskilab/VizCNV Fork of cluhaowie/VizCNV

cancerbits/shahin2021_ikzf2_het 📦