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    41 repositories

    • cigarmath

      Public
      A collection of python utilities for manipulating CIGARS.
      MIT License
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • ice

      Public
      Synthego ICE - Inference of CRISPR Editing software
      Python
      •
      Other
      •31•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • quantitative-reasoning-in-biology

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 1, 2025Jan 1, 2025

    • OMICS

      Public
      Repo for students of the Advanced OMICS Course
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •18•12•0•0•Updated Dec 19, 2024Dec 19, 2024

    • pod5-file-format

      Public
      Pod5: a high performance file format for nanopore reads.
      C++
      •
      Other
      •19•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • Cas_HIV_hits

      Public
      Scripts and figures for Frontiers Manuscript.
      Jupyter Notebook
      •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • the-littlest-jupyterhub

      Public
      Simple JupyterHub distribution for 1-100 users on a single server
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •349•1•0•0•Updated Sep 2, 2022Sep 2, 2022

    • HIV-Quasipore-basecallers

      Public
      Other
      •0•6•0•0•Updated Jun 5, 2022Jun 5, 2022

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      Python
      •
      Mozilla Public License 2.0
      •8•1•0•0•Updated May 18, 2022May 18, 2022

    • hiv-transformers

      Public
      A collection of Hugging Face tools for analyzing HIV
      Jupyter Notebook
      •0•2•0•0•Updated Apr 11, 2022Apr 11, 2022

    • Neurocog_Tat-miRNA_binding_analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • DL_RPI_prediton_benchmak

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • SAE-based_RPI_negative_sample_generation

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2021Aug 28, 2021

    • pbmeth

      Public
      PacBio CpG Methylation prediction using Fast.ai
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • artic-ncov2019

      Public
      ARTIC nanopore protocol for nCoV2019 novel coronavirus
      Python
      •
      Creative Commons Attribution 4.0 International
      •165•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • pipeline-multitool

      Public
      Python
      •0•0•0•0•Updated Nov 3, 2020Nov 3, 2020

    • nbdev_template

      Public template
      Template for nbdev projects
      Jupyter Notebook
      •
      Apache License 2.0
      •99•0•0•0•Updated Sep 15, 2020Sep 15, 2020

    • HIV-nanopore-pipeline

      Public
      HIV-specific nanopore sequencing pipeline
      Python
      •0•1•0•0•Updated Sep 2, 2020Sep 2, 2020

    • htguideseq

      Public
      High Throughput GuideSeq Analysis
      Dockerfile
      •0•1•0•0•Updated Sep 1, 2020Sep 1, 2020

    • HIV-subtype-gRNAs

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 5, 2020Jul 5, 2020

    • RPI-DL-Architecture-Review

      Public
      Holds all models, weights, scripts, etc. used to compare RPI DL architectures
      Jupyter Notebook
      •0•0•0•0•Updated Jul 5, 2020Jul 5, 2020

    • nanopore-analysis

      Public
      Basic Nanopore Snakemakes for Nanopore analysis
      Shell
      •0•0•0•0•Updated Jun 29, 2020Jun 29, 2020

    • DeepLabCut

      Public
      Markerless pose estimation of user-defined features with deep learning for all animals, including humans
      Python
      •
      GNU Lesser General Public License v3.0
      •1.7k•0•0•0•Updated Jan 8, 2020Jan 8, 2020

    • Genomic-ULMFiT

      Public
      ULMFiT for Genomic Sequence Data
      Jupyter Notebook
      •55•0•0•0•Updated Nov 15, 2019Nov 15, 2019

    • chroCRISPR

      Public
      Analysis scripts for Molecular Therapy paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 24, 2019Oct 24, 2019

    • hiv-crispr-cards

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 9, 2019Aug 9, 2019

    • Mask_RCNN

      Public
      Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
      Python
      •
      Other
      •12k•0•0•0•Updated Jul 18, 2019Jul 18, 2019

    • Tat-length-analysis

      Public
      Repo for: "Investigating the distribution of HIV-1 Tat lengths present in the Drexel Medicine CARES cohort"
      Jupyter Notebook
      •0•0•0•0•Updated Jun 10, 2019Jun 10, 2019

    • journalclub

      Public
      Repo for Dampier computational journal club
      HTML
      •
      MIT License
      •4•5•0•0•Updated Apr 1, 2019Apr 1, 2019

    • gpt-2

      Public
      Code for the paper "Language Models are Unsupervised Multitask Learners"
      Python
      •
      MIT License
      •5.6k•0•0•0•Updated Mar 8, 2019Mar 8, 2019