Heart is a project working directly with the LA City Attorney’s Homeless Engagement and Response Team. We are building a database and case management system to streamline their workflow and enable them to scale their program. Find us on the Hack for LA Slack #heart.
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Genotype + Environment = Trait Evidence (GET-E) Database: help the Personal Genome Project, the clinical genetics community, and, the general public interpret individual genomes.
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RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
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HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
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Expression Atlas
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de novo assembly of RNA-seq data using ABySS
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a hidden Markov model to infer simple repeats from genome sequences
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gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
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visualize CNV data from targeted capture based sequencing data
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Assembling the cause of phenotypes and genotypes from NGS data
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Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)
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GlucoSym is an open-source simulator aimed to help in the testing and development of insulin delivery automation systems.
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Backup Ceph's RBD on Ceph, with Proxmox integration
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Create a report of Netbox site with IP, VLANs, and prefixes
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Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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Open source Java library for computational proteomics
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Medical Relations and Entities Extraction
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Predict plasmids from uncorrected long read data
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small rna-seq analysis package
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SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.
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The script presents a simple way to visualize features on human chromosome ideograms
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[EBioMedicine] Deep-learning-assisted detection and segmentation of rib fractures from CT scans: Development and validation of FracNet
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Genomic data integration platform
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<<------ Use SnapATAC!!
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PathOS is a clinical application for filtering, analysing and reporting on NGS variants
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Helping spread communication about novel virus Covid-19 via FREE text messages for everyone.
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Weak supervision methods for extracting real world evidence from EHRs
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Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
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An Interactive Cell for the Web(GL)
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Coronavirus Monitor Web App with latest news, current cases, etc.
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Source code for ProteGO Safe PWA
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Extension library for the Varian Eclipse Scripting API
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Predict mutated T-cell epitopes from sequencing data
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Example client programs for Saphetor's VarSome annotation API
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3D printed sculpture of a DNA molecule, showing my own genome
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A tool to genotype CYP2D6 with WGS data
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Platform for Calcium Imaging analysis
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Site Identification from Short Read Sequences.
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LOFAR pipeline using killms/ddfacet
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pipeline-nanopore-ref-isoformsby nanoporetech
Python 
22 Version:Current License: Proprietary (Proprietary)
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
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heartby hackforla
Heart is a project working directly with the LA City Attorney’s Homeless Engagement and Response Team. We are building a database and case management system to streamline their workflow and enable them to scale their program. Find us on the Hack for LA Slack #heart.
JavaScript 27Updated: 3 y ago License: Permissive (MIT)
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MRNetby MisaOgura
PyTorch implementation of the MRNet paper, developed for the MRNet Competition hosted by the Stanford ML Group
Python 27Updated: 3 y ago License: Permissive (MIT)
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get-evidenceby tomclegg
Genotype + Environment = Trait Evidence (GET-E) Database: help the Personal Genome Project, the clinical genetics community, and, the general public interpret individual genomes.
Python 26Updated: 3 y ago License: Proprietary (Proprietary)
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radiaby aradenbaugh
RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
Python 26Updated: 3 y ago License: Strong Copyleft (AGPL-3.0)
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CNCIby www-bioinfo-org
Coding-Non-Coding Index (CNCI)
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patient_similarityby yinchangchang
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VICTREby DIDSR
Virtual Imaging Clinical Trial for Regulatory Evaluation
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FeGenieby Arkadiy-Garber
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
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the-art-genome-projectby artsy
Gene names and definitions
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covid19kgby covid19kg
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
Python 26Updated: 3 y ago License: Permissive (CC0-1.0)
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atlasby ebi-gene-expression-group
Expression Atlas
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transabyssby bcgsc
de novo assembly of RNA-seq data using ABySS
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medisimby babylonhealth
Medical Similarity Dataset creation from SNOMED
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RepeatHMMby WGLab
a hidden Markov model to infer simple repeats from genome sequences
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gemBSby heathsc
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
Python 25Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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reconCNVby rghu
visualize CNV data from targeted capture based sequencing data
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plasmidtronby sanger-pathogens
Assembling the cause of phenotypes and genotypes from NGS data
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Phen2Geneby WGLab
Phenotype driven gene prioritization for HPO
Python 25Updated: 3 y ago License: Permissive (MIT)
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genipeby pgxcentre
Genome-wide imputation pipeline
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BioPosDepby datquocnguyen
Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)
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GlucoSymby Perceptus
GlucoSym is an open-source simulator aimed to help in the testing and development of insulin delivery automation systems.
JavaScript 25Updated: 3 y ago License: No License (No License)
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backurneby JackSlateur
Backup Ceph's RBD on Ceph, with Proxmox integration
Python 25Updated: 3 y ago License: Strong Copyleft (GPL-2.0)
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netbox_rich_reportby routetonull
Create a report of Netbox site with IP, VLANs, and prefixes
Python 24Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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gff3toemblby sanger-pathogens
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Python 24Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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compomics-utilitiesby compomics
Open source Java library for computational proteomics
Java 24Updated: 2 y ago License: Permissive (Apache-2.0)
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medknowby kbogas
Medical Relations and Entities Extraction
Python 24Updated: 3 y ago License: Permissive (Apache-2.0)
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tiptoftby andrewjpage
Predict plasmids from uncorrected long read data
Python 24Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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smallrnaseqby dmnfarrell
small rna-seq analysis package
Python 24Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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SNPbinnerby solgenomics
SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.
Python 24Updated: 1 y ago License: No License (No License)
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tagoreby jordanlab
The script presents a simple way to visualize features on human chromosome ideograms
Python 24Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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FracNetby M3DV
[EBioMedicine] Deep-learning-assisted detection and segmentation of rib fractures from CT scans: Development and validation of FracNet
Python 24Updated: 3 y ago License: Permissive (Apache-2.0)
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gediby erhard-lab
Genomic data integration platform
Java 23Updated: 1 y ago License: Permissive (Apache-2.0)
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PathOSby PapenfussLab
PathOS is a clinical application for filtering, analysing and reporting on NGS variants
Java 23Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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covid-helplineby Marwan01
Helping spread communication about novel virus Covid-19 via FREE text messages for everyone.
Python 23Updated: 4 y ago License: Permissive (MIT)
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ehr-rweby som-shahlab
Weak supervision methods for extracting real world evidence from EHRs
Python 23Updated: 3 y ago License: Permissive (Apache-2.0)
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MGSEby bpucker
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
Python 23Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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biorenderby thejmazz
An Interactive Cell for the Web(GL)
JavaScript 23Updated: 4 y ago License: No License (No License)
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Coronavirus-Live-Monitorby xtrp
Coronavirus Monitor Web App with latest news, current cases, etc.
JavaScript 23Updated: 4 y ago License: Permissive (MIT)
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webby ProteGO-Safe
Source code for ProteGO Safe PWA
JavaScript 23Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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ESAPIXby rexcardan
Extension library for the Varian Eclipse Scripting API
C# 23Updated: 3 y ago License: Permissive (MIT)
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topiaryby openvax
Predict mutated T-cell epitopes from sequencing data
Python 22Updated: 3 y ago License: Permissive (Apache-2.0)
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varsome-api-client-pythonby saphetor
Example client programs for Saphetor's VarSome annotation API
Python 22Updated: 2 y ago License: Permissive (Apache-2.0)
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SPeWby NCBI-Hackathons
Automatic Packaging and Distribution of Bioinformatics Pipelines
Python 22Updated: 3 y ago License: Permissive (MIT)
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dna-sculptureby PaulKlinger
3D printed sculpture of a DNA molecule, showing my own genome
Python 22Updated: 4 y ago License: Permissive (MIT)
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Cyriusby Illumina
A tool to genotype CYP2D6 with WGS data
Python 22Updated: 3 y ago License: Permissive (Apache-2.0)
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MESmerizeby kushalkolar
Platform for Calcium Imaging analysis
Jupyter Notebook 22Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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SISRSby rachelss
Site Identification from Short Read Sequences.
Python 22Updated: 3 y ago License: No License (No License)
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ddf-pipelineby mhardcastle
LOFAR pipeline using killms/ddfacet
Python 22Updated: 11 mo ago License: Strong Copyleft (GPL-2.0)
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pipeline-nanopore-ref-isoformsby nanoporetech
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
Python 22Updated: 3 y ago License: Proprietary (Proprietary)
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