mdperry

mdperry's Stars

• ucscGenomeBrowser/cellBrowser

  Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

  Language:JavaScript8

• maximilianh/cellBrowser

  main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

  Language:JavaScript10240

• corneliusroemer/pango-sequences

  Consensus sequences for each Pango lineage

  Language:Python181

• tomwenseleers/LineageExplorer

  Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline fits

  Language:R244

• johnkerl/miller

  Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

  Language:Go8.7k207

• pha4ge/pipeline-resources

  Bioinformatics Pipeline and Visualization resources

  4927

• saiftynet/Wordle

  A command Line wordle clone

  Language:Perl29

• cov-lineages/pango-designation

  Repository for suggesting new lineages that should be added to the current scheme

  Language:Jupyter Notebook1k97

• maximilianh/multiSub

  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

  Language:Python352

• EddyRivasLab/infernal

  RNA secondary structure/sequence profiles for homology search and alignment

  Language:C10023

• jts/ncov-tools

  Small collection of tools for performing quality control on coronavirus sequencing data and genomes

  Language:Python4616

• broadinstitute/genomics-in-the-cloud

  Source code and related materials for the O'Reilly book

  Language:Jupyter Notebook8926

• andersen-lab/ivar

  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

  Language:C++11539

• virusseq/portal-ui

  Canadian VirusSeq Data Portal

  Language:TypeScript88

• HormozdiariLab/TAD-fusion-score

  Language:C++72

• akdemirlab/HiCPlotter

  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

  Language:Python17679

• geoffswc/MongoDB-Python-Workshop

  Workshop notebooks and material for building, populating, and reading data from MongoDB

  Language:Jupyter Notebook31

• DavidQuigley/WCDT_WGBS

  West Coast Dream Team Whole Genome Bisulfite Sequencing

  Language:R154

• opencb/opencga

  An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is maintained and develop by its parent company Zetta Genomics. Please contact support@zettagenomics.com for bug report and feature requests.

  Language:Java16497

• igneous-systems/md5vec

  AVX-accelerated 8-way parallel md5

  Language:Go253

• taoliu/HMMRATAC

  HMMRATAC peak caller for ATAC-seq data

  Language:Java1

• apache/mxnet

  Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more

  Language:C++20.7k6.8k

• ljdursi/ML-for-scientists

  Machine Learning for Scientists Tutorial

  Language:Python347

• JoachimGoedhart/PlotsOfDifferences

  Shiny App for comparison of samples and plotting effect size

  Language:R287

• politza/pdf-tools

  Emacs support library for PDF files.

  Language:C1.6k162

• norvig/paip-lisp

  Lisp code for the textbook "Paradigms of Artificial Intelligence Programming"

  Language:Common Lisp7.1k702

• WGLab/LinkedSV

  Language:C218

• Illumina/Nirvana

  The nimble & robust variant annotator

  Language:C#16644

• cc2qe/vawk

  An awk-like VCF parser

  Language:Python5412

• 10XGenomics/longranger

  10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling

  Language:Python304