JamieCFreeman

JamieCFreeman's Stars

• cmdcolin/awesome-genome-visualization

  A list of interesting genome browser and genome visualization programs

  Language:TypeScript8812810112

• oushujun/EDTA

  Extensive de-novo TE Annotator

  Language:Perl3541151574

• RealTimeGenomics/rtg-tools

  RTG Tools: Utilities for accurate VCF comparison and manipulation

  Language:Java30422048

• PhanstielLab/plotgardener

  Language:R30389028

• alekseyzimin/masurca

  Language:M42481634635

• popgenmethods/lecture_notes

  Lecture Notes on Computational and Mathematical Population Genetics

  18719015

• mkirsche/Jasmine

  Jasmine: SV Merging Across Samples

  Language:Java186115818

• DReichLab/EIG

  Eigen tools by Nick Patterson and Alkes Price lab

  Language:C181179760

• KolmogorovLab/Severus

  A tool for somatic structural variant calling using long reads

  Language:Python1065335

• mahulchak/svmu

  A program to call variants from genome alignment

  Language:C++7652718

• brentp/vcfexpress

  expressions on VCFs

  Language:Rust65201

• dantaki/SV2

  Support Vector Structural Variation Genotyper

  Language:Python5863011

• jwfoley/bioanalyzeR

  R tools for Agilent electrophoresis data

  Language:R446234

• SouthGreenPlatform/culebrONT

  A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

  Language:Python3617128

• SBIMB/StellarPGx

  Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.

  Language:Python304357

• tskit-dev/pyslim

  Tools for dealing with tree sequences coming to and from SLiM.

  Language:Python27620623

• ACAD-UofA/Guide-to-manipulating-PLINK-EIG-and-VCF-files

  A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

  Language:Shell18212

• sanjaynagi/rna-seq-pop

  Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

  Language:Jupyter Notebook182819

• ThibaultLeroyFr/Intro2PopGenomics

  Leroy & Rougemont - “learning-by-doing” introduction to population genomics - scripts

  Language:Shell18107

• zxc307/GWAS_simulation_handbook

  9201

• mahulchak/dspr-asm

  Contains scripts and programs used to generate assemblies and variants for the DSPR project

  Language:R8314

• justin-lack/Drosophila-Genome-Nexus

  The Drosophila Genome Nexus is a repository of more than 600 Drosophila melanogaster genomes from Africa, Europe, and North America. All scripts and pipeline commands used to generate these genome sequences are available here.

  Language:Perl7425

• laulabbrandeis/TIDAL

  Transposon Insertion and Depletion AnaLyzer

  Language:C6238

• NAL-i5K/NAL_RNA_seq_annotation_pipeline

  Language:Python53374

• ybrandvain/biostat

  Language:HTML5342

• DworkinLab/EvolveResequencePipeline

  This is a repository that provides an overview, scripts, and helpful hints for doing our evolve and resequence analysis

  41301

• runxi-shen/Predict-Genomic-Resolution-of-BSA

  This repository stores the codes that run SLiM simulations and plot the graphs for the paper that derives the analytical solution for genomic resolution of Bulk Segregant Analysis (BSA).

  Language:Jupyter Notebook3100

• dantaki/Local-De-Novo-Assembly-with-Long-Reads

  A quick tutorial on local de novo assembly of long reads

  2200

• Mduranton/simulations_introgression_recombination

  Language:R2101

• dliang5/breakpoint-assembly

  Language:Python1201