KarchinLab/open-cravat

A modular annotation tool for genomic variants

Language: JavaScript - Size: 8.78 MB - Last synced: about 14 hours ago - Pushed: about 15 hours ago - Stars: 106 - Forks: 26

SlowSD/Tutorial-Next-Generation-Sequence-Analysis

This repository summarizes complete NGS analysis for a beginner.

Size: 1.65 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

gauravcodepro/odd-ratio-estimator

This function will take a data frame of the outbreak and will predict the odd ratios and the specific likelihood of occurrence of the disease in that specific geographical location

Language: Python - Size: 18.6 KB - Last synced: 3 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

INMEGEN/Pipelines_INMEGEN

Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.

Language: Nextflow - Size: 3.06 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 7 - Forks: 0

gauravcodepro/slurm-pbs

slurm and pbs scripts for illumina and long read genome assembly, transcriptome, metagenomics and comparative analysis

Language: Shell - Size: 76.2 KB - Last synced: 3 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

Language: HTML - Size: 9.68 MB - Last synced: 4 days ago - Pushed: 9 days ago - Stars: 57 - Forks: 22

mt1022/gppy

[G]enomic [P]ositioning with [Py]thon

Language: Python - Size: 2.98 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 7 - Forks: 1

bcgsc/ntRoot

🌳 Human ancestry inference from genomic data

Language: Python - Size: 21.6 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 0

genular/pandora

PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:

Language: Vue - Size: 16 MB - Last synced: 8 days ago - Pushed: 18 days ago - Stars: 133 - Forks: 20

pfeiferd/genestrip

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

Language: Java - Size: 69.7 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 3 - Forks: 0

Matthew-Mosior/Basic-Variant-Tools

Command-line toolkit for genomic datasets.

Language: Haskell - Size: 81.1 KB - Last synced: 16 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

FunctionLab/selene

a framework for training sequence-level deep learning networks

Language: Jupyter Notebook - Size: 151 MB - Last synced: 6 days ago - Pushed: 6 months ago - Stars: 364 - Forks: 86

ikergarcia1996/Gene2Tab

This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.

Language: Python - Size: 28.3 KB - Last synced: 21 days ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

Cloud-SPAN/00genomics

Genomics Course Introduction

Language: Python - Size: 64.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

zhaoxiaofei/bindash

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

Language: C++ - Size: 985 KB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 51 - Forks: 7

laurentnoe/yass

genomic alignment similarity search tool

Language: C - Size: 496 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 17 - Forks: 6

xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Language: Python - Size: 43.7 MB - Last synced: 15 days ago - Pushed: 9 months ago - Stars: 9 - Forks: 2

CBIIT/Misteli-Lab-CCR-NCI

Collection of statistical scripts, image analysis workflows, data used in publications by the Misteli Lab.

Language: HTML - Size: 69.6 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 15 - Forks: 3

sooraj14072001/TEAM-GENOMICS-ONE

Team Genomics One is a group of Bioinformatics enthusiasts gathered together from around the globe , to learn and move forward in solving biological myths by analyzing various types of biological data. We believe Team Work is Dream Work!!!

Size: 2.83 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

ovsama/Genomic_Data_Science

Here is a whole bunch of genomic data analyses using Bioconductor packages. The files are found in the form of .R files.

Language: R - Size: 178 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

bobeobibo/phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

Language: HTML - Size: 6.8 MB - Last synced: 24 days ago - Pushed: 4 months ago - Stars: 46 - Forks: 15

icaromsc/WGCA

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

Language: Python - Size: 629 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 2

MaryAgopian/Variant_Barcoding_M.orygis

Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

Language: R - Size: 55.7 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

shilab/DP-MIA Fork of work-hard-play-harder/DP-MIA

Differential Privacy Protection against MembershipInference Attack on Machine Learning for Genomic Data

Language: Python - Size: 2.39 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 13 - Forks: 3

mrdanieleze/Genomic-Sequence-Comparison-Code-GSCC-

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

Language: Python - Size: 26.4 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: TypeScript - Size: 124 MB - Last synced: 7 days ago - Pushed: 11 days ago - Stars: 83 - Forks: 37

LilQuacky/covid-genome-variation

A Python script that uses MAFFT to align SARS-CoV-2 genomes with respect to the reference genome, identifying and reporting pointwise variations compared to the reference, along with comparative statistics on the analyzed genomes.

Language: Python - Size: 160 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

aliafzal/Identification-of-mislabeling-data-using-ML

Overcome mislabeling errors in genomics training sets by utilizing machine learning on AWS EC2 and Apache Spark.

Language: Jupyter Notebook - Size: 28.4 MB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

hsaxe/Omics-Analyst

R package to facilitate omics analyses

Language: R - Size: 50.8 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

mattssca/BioMaesteR

R package with convenience functions commonly requested in various types of genomic analysis within R.

Language: R - Size: 95.2 MB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

adeschen/consensusSeekeR

This R package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. Tested on ChIP-Seq peaks and nucleosome positions.

Language: R - Size: 9.06 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

Shaked35/Genome-AC-GAN

This repository provides tools to train and evaluate the Genome-AC-GAN model for generating realistic artificial human genomes.

Language: Jupyter Notebook - Size: 105 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

ccneko/OMACASE

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities

Language: Python - Size: 2.74 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

JoachimGoedhart/VolcaNoseR

Shiny app for making and annotating Volcano plots

Language: R - Size: 472 KB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 17 - Forks: 7

biomguler/G-WASPiper

This repository is my collection of pipelines for basic GWAS analysis, written in R to simplify, please cite original tools/approaches referred in the pipelines.

Language: R - Size: 5.41 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: HTML - Size: 68.5 MB - Last synced: 7 days ago - Pushed: about 1 month ago - Stars: 9 - Forks: 38

muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Language: C++ - Size: 149 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 55 - Forks: 10

rjdkmr/gcMapExplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

Language: Python - Size: 5.05 MB - Last synced: 21 days ago - Pushed: over 2 years ago - Stars: 21 - Forks: 9

Daylily-Informatics/daylily

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Language: Python - Size: 290 MB - Last synced: 3 months ago - Pushed: 7 months ago - Stars: 17 - Forks: 0

Cloud-SPAN/02genomics

Data preparation and organisation

Language: Python - Size: 51.2 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Cloud-SPAN/01genomics

Project management for cloud genomics

Language: Python - Size: 5.6 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced: 5 months ago - Pushed: 11 months ago - Stars: 4 - Forks: 2

epiviz/epivizFileServer

Python library to query and transform genomic data from indexed files

Language: Python - Size: 16.7 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 4

jlt3/ERCEs_2023

Scripts from Turner et al 2023 "Master transcription factor binding sites are necessary for early replication control element activity"

Language: Shell - Size: 5.86 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

HuntsmanCancerInstitute/GQuery

GQuery is a software tool for rapidly querying large numbers of bgzip compressed, tabix indexed genomic data files e.g. vcf, maf, bed, bedGraph, etc. from multiple species with different genome builds without the need to develop, debug, and maintain custom file parsers. Search for particular germline or somatic mutations, copy number changes, differentially expressed genes, epigenetic marks, anything that can be associated with genomic coordinates. Just point the GQuery indexer at a collection of tabix indexed files and then run either the GQuery command line app or the web API to search them. GQuery is built using a fast, multi-threaded, genomic range search engine with extensive junit testing.

Language: C - Size: 4.69 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

JuhunC/NICER

NICE Renew

Language: HTML - Size: 2.19 GB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 2

gdurif/pCMF

pCMF R package

Language: C++ - Size: 271 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 11 - Forks: 0

cellular-genomics/cluster-paired-end-tags

Script to cluster Paired End Tags (PETs) from chromatin conformation capture (3C) experiments

Language: Python - Size: 251 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 1

rbr7/bioinformatics_courses

A repository for maintaining assignments and projects, from courses done in bioinformatics and CB.

Language: Jupyter Notebook - Size: 10.4 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

D4GEN-Genopole/GARDS-CHSF

Méthodes pour la FAIRification des (méta) données Omics - Projet porté par Mohanad MAHFOUD - CHSF

Size: 2.49 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

yumatchlab/solidity-stringutils Fork of sensecollective/solidity-stringutils

Basic string utilities for Solidity

Size: 18.6 KB - Last synced: 7 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

alexjschiffer/AutoEmma

Automated Efficient Mixed Model Association Studies - R Package

Language: R - Size: 15.1 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

thierrygosselin/stackr

stackr: an R package to run stacks software pipeline

Language: R - Size: 17.7 MB - Last synced: 4 days ago - Pushed: over 3 years ago - Stars: 26 - Forks: 8

revaoleg/SeqWord

Programs for genomic, genome linguistics and metagenomics

Size: 13.7 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

Sentieon/sentieon-google-genomics

Run Sentieon pipelines on Google Cloud Platform

Language: Shell - Size: 126 KB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 5 - Forks: 7

hyperbrowser/genomic-hyperbrowser Fork of elixir-oslo/proto

The GSuite HyperBrowser - the new version of the Genomic HyperBrowser, currently forked from Galaxy v16.01

Language: Python - Size: 364 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 2 - Forks: 1

Byronxy/GEO

learn R by rote

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kishwarshafin/helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Language: Python - Size: 7.27 MB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 68 - Forks: 9

thierrygosselin/grur

grur: an R package tailored for RADseq data imputations

Language: R - Size: 7.46 MB - Last synced: 4 days ago - Pushed: over 3 years ago - Stars: 7 - Forks: 0

HannahVMeyer/LiMMBoAnalysis

Language: R - Size: 8.47 MB - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 0

ValeriaP5/Peculiar-Statistics-of-the-Forward-and-Reverse-Half-Strands

Python applications to Genomics

Size: 2.93 KB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

uab-cgds-worthey/DITTO4NF

Easy to use web interface for biologists to look for NF1 variants and understand their deleteriousness using DITTO scores.

Language: Jupyter Notebook - Size: 206 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

kaymers/MetaG

MetaG is a comprehensive metagenomic visualization tool. MetaG displays lower dimensional representations of high throughput metagenomic sequence reads using deep-learning techniques. MetaG will provide additional taxonomic details of the composition of a given metagenome using its pipeline based on BLAST.

Language: Python - Size: 11.1 MB - Last synced: 9 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

mtsz-thiago/AnGRA

Biblioteca para análise de genômica de resistência a antibióiticos.

Language: Dockerfile - Size: 825 KB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

fjdf/slaMEM

Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array

Language: C - Size: 566 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 10 - Forks: 5

Pintaius/LDmergeFM

Generating a weighed average of LDSTORE matrices for locus-based fine-mapping.

Language: R - Size: 736 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

ishamada/bioiX

PCA on Genotypes

Language: Python - Size: 1.73 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 0

snystrom/vplot

A commandline tool for generating vplot matrices from paired end sequencing data such as MNase-seq, ATAC-seq, or CUT&RUN.

Language: Rust - Size: 134 KB - Last synced: about 13 hours ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1

TomKellyGenetics/graphsim

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

Language: R - Size: 35.8 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 21 - Forks: 7

jakublipinski/build-deepsea-training-dataset

Build DeepSea training dataset from raw data

Language: Python - Size: 13.9 MB - Last synced: 9 months ago - Pushed: 10 months ago - Stars: 14 - Forks: 1

bernatgel/regioneR

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests

Language: R - Size: 1.16 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 11 - Forks: 3

PlantDr430/CSU_scripts

Scripts created at CSU as a PhD student for genomic annotations and comparisons.

Language: Python - Size: 172 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

programerkotik/Cancer-Genomics-Data-Analysis

Cancer Genomics Data Analysis exercise for the course Analytical Methods in Cancer Genomics 2023. The goal of the exercise is to generate a read-depth plot for human cancer sample.

Language: Python - Size: 190 KB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

strumenti-formali-per-la-bioinformatica/tumor-classification

[a.a. 22/23] G. Antonucci, N. Pagliara

Language: TeX - Size: 24.1 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

gnoanto94/tumor-classification

[a.a. 22/23] G. Antonucci, N. Pagliara

Language: Python - Size: 3.3 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

thierrygosselin/gotedna

Guidance on optimal eDNA sampling periods to develop, optimize and interpret monitoring programs

Language: R - Size: 860 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

Poissonfish/iPat

iPat allows you to perform GWAS and GS with drags and clicks!

Language: Java - Size: 128 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 2

andrealauria104/ngsRtools

A Suite of R Packages for NGS-based Epigenomic Data Analysis.

Language: R - Size: 714 KB - Last synced: 23 days ago - Pushed: about 1 year ago - Stars: 2 - Forks: 1

deprodas/Statistical-Genomics-BMBDU

Repository to support my classmates with their Master's Thesis project at BMB-DU.

Language: R - Size: 11.7 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

cellular-genomics/python-FIREcaller

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

Language: Python - Size: 21.5 KB - Last synced: 14 days ago - Pushed: about 2 years ago - Stars: 4 - Forks: 1

guillaume-gricourt/HmnTrimmer

Fast-polyvalent trimmer used for several applications of next-generation sequencing

Language: HTML - Size: 11.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

sooraj14072001/TEAM-GENOMICS_ONE

Team Genomics One is a group of Bioinformatics enthusiasts gathered together from around the globe , to learn and move forward in solving biological myths by analyzing various types of biological data. We believe Team Work is Dream Work!!!

Size: 2.56 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

genomematt/xenomapper2

A utility for splitting mixed origin NGS reads with secondary or alt mappings

Language: Python - Size: 1.04 MB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

linas/biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

Language: Scheme - Size: 14.2 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 4 - Forks: 0

BCCDC-PHL/ncov-recombinant-nf

Nextflow wrapper for ktmeaton/ncov-recombinant

Language: Python - Size: 36.1 KB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

tanaylab/misha

Genomic data analysis suite

Language: C++ - Size: 27.6 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 1

dgreenhoe/symbolic-sequence-processing

C++ code for symbolic sequence processing, including genomic sequence processing (GSP)

Language: C++ - Size: 770 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

BrianSanderson/salix-nigra-slr

Bioinformatic pipeline for genetic mapping using a novel genome sequencing platform

Language: Jupyter Notebook - Size: 2.55 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

BrianSanderson/phylo-seq-cap

Bioinformatic pipeline for phylogenetics and population genomics using a novel genome sequencing platform

Language: Jupyter Notebook - Size: 2.14 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

gibbslab/biobash Fork of ampinzonv/biobash

Common BASH routines for computational biology

Language: Shell - Size: 17.6 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 3

AndroidSim/Bioinformatics

A collection of projects in bioinformatics.

Language: C - Size: 5.43 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

CEA-LIST/sgntx

iDASH 2017 competition, track 2 winning team solution

Language: Rust - Size: 45.9 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 8 - Forks: 0

yaan-jang/leri

Leri Analytics delivers bioinformatics services for and solutions to both the academic labs and industries.

Size: 285 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

biodata-fun/htslib_howto

Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts

Language: C - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 11 - Forks: 1

hernanmd/Booklet-DNA Fork of SquareBracketAssociates/Booklet-DNA

Bioinformatics with Pharo

Language: CSS - Size: 2.79 MB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

BiCroLab/blissNP

Step-by-step procedure for the analysis of BLISS and sBLISS datasets. For more information:

Language: Shell - Size: 310 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 2

CMU-SAFARI/SNP-Selective-Hiding

An optimization-based mechanism :dna: :closed_lock_with_key: to selectively hide the minimum number of overlapping SNPs among the family members :family_man_woman_girl_boy: who participated in the genomic studies (i.e. GWAS). Our goal is to distort the dependencies among the family members in the original database for achieving better privacy without significantly degrading the data utility.

Language: MATLAB - Size: 6.98 MB - Last synced: 13 days ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1

Noam-Hadar/BAMdelbee

BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the ones in question. We hereby demonstrate how our application can spot homozygous deletions absent from VCF files for being too vast, yet undetectable by chromosomal microarrays (CMA) for being too small. The application is freely available on our website and can run on a common laptop. Therefore, we recommend integrating it into WES and WGS interpretation pipelines for recessive diseases.

Language: Python - Size: 39.8 MB - Last synced: 12 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

daormar/flux-capacitor

Flux Capacitor toolkit for systems biology

Language: Python - Size: 85.1 MB - Last synced: 5 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

joycewang914/Genomic_and_Patient_Transfer_Analyasis_of_Resistant_Bacteria

Active surveillance of newly-admitted nursing home patients for colonization of antibiotic-resistant bacteria reveals that multiple lineages have spread across southeast Michigan healthcare networks.

Language: R - Size: 9.58 MB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0