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Achievements

Achievement: Arctic Code Vault ContributorAchievement: Starstruckx2Achievement: Pull Shark

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  • cylinter Public

    Forked from labsyspharm/cylinter

    An Interactive Image Segmentation Filter for Multiplex Microscopy

    Python MIT License Updated Dec 30, 2024

  • brd4-analysis Public

    Analysis of BRD4 expression in cancer

    MIT License Updated Dec 5, 2024

  • svaba Public

    Structural variation and indel detection by local assembly

    c-plus-plus variants structural-variations indels assembled-contigs
    C++ 239 45 GNU General Public License v3.0 Updated Nov 19, 2024

  • cyftools Public

    CLI tools for CyCIF

    Python 3 Updated Sep 21, 2024

  • SeqLib Public

    C++ htslib/bwa-mem/fermi interface for interrogating sequence data

    c-plus-plus sequence-alignments htslib bwa-mem fermi
    C++ 136 36 Other Updated Aug 9, 2024

  • bwa Public

    Forked from lh3/bwa

    Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

    C 2 Apache License 2.0 Updated May 18, 2024

  • fermi-lite Public

    Forked from lh3/fermi-lite

    Standalone C library for assembling Illumina short reads in small regions

    C 1 MIT License Updated May 5, 2024

  • cytif Public

    Command line tools for image processing using libvips

    C++ Updated Mar 21, 2024

  • VariantBam Public

    Filtering and profiling of next-generational sequencing data using region-specific rules

    Makefile 74 10 Other Updated Oct 30, 2023

  • cyslib Public

    Forked from samtools/htslib

    C library for high-throughput multiplex imaging data formats

    C Other Updated Aug 18, 2023

  • KDTree Public

    Forked from crvs/KDTree

    Simple C++ KD-Tree implementation

    C++ 2 2 BSD 3-Clause "New" or "Revised" License Updated Aug 17, 2023

  • cycifr Public

    R package for processing highly multiplexed spatial imaging data (e.g. CyCIF)

    Python MIT License Updated Feb 24, 2023

  • libtiff Public

    Forked from vadz/libtiff

    OBSOLETE and not updated any more libtiff mirror, see website for the new one

    C Other Updated Feb 6, 2023

  • carreview Public

    Manubot CAR-T Review Paper

    HTML Other Updated Jan 29, 2023

  • lattice Public

    Forked from broadinstitute/lattice
    HTML BSD 3-Clause "New" or "Revised" License Updated Jun 26, 2022

  • aws-cli-user-guide Public

    Forked from awsdocs/aws-cli-user-guide

    The open source version of the AWS CLI User Guide

    Other Updated Mar 19, 2021

  • setup Public

    Useful customizations of a unix environment

    Emacs Lisp 1 Updated Jan 8, 2021

  • us-potus-model Public

    Forked from TheEconomist/us-potus-model

    Code for a dynamic multilevel Bayesian model to predict US presidential elections. Written in R and Stan.

    HTML MIT License Updated Jun 11, 2020

  • varval Public

    Rearrangement validation through targeted sequence realignment

    C++ 3 GNU General Public License v2.0 Updated Apr 18, 2019

  • roverlaps Public

    Fast and memory efficient genomic range overlaps for R

    C++ 4 Other Updated Feb 20, 2019

  • seqtools Public

    Basic command-line sequence analysis utilities I can't find elsewhere

    C++ 2 MIT License Updated Feb 13, 2019

  • bxtools Public

    Tools for analyzing 10X Genomics data

    genomics sequencing tenxgenomics
    Makefile 42 10 MIT License Updated Feb 6, 2019

  • fishHook Public

    Forked from mskilab-org/fishHook

    R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

    R Updated Nov 6, 2018

  • ensapi Public

    Command-line interface to Ensembl REST API

    C++ Updated Oct 9, 2018

  • gTrack Public

    Forked from mskilab-org/gTrack

    R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

    R Updated Sep 27, 2018

  • jUtils Public

    R utilities and shortcuts

    R MIT License Updated May 10, 2018

  • SVsig Public

    Forked from ofershapira/SVsig

    Recurrent structural variations detection in cancer whole genomes

    MATLAB 1 1 Updated Feb 9, 2018

  • ncbitax2lin Public

    Forked from zyxue/ncbitax2lin

    Convert NCBI taxonomy dump into lineages

    Python MIT License Updated Oct 16, 2017

  • freebayes Public

    Forked from freebayes/freebayes

    Bayesian haplotype-based polymorphism discovery and genotyping.

    C++ MIT License Updated Apr 25, 2017

  • walaj.github.io Public

    Forked from academicpages/academicpages.github.io

    Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

    JavaScript 1 MIT License Updated Mar 28, 2017