jluebeck

jluebeck's Stars

• chrislgarry/Apollo-11

  Original Apollo 11 Guidance Computer (AGC) source code for the command and lunar modules.

  Language:Assembly57.1k1.3k3796.8k

• streamlit/streamlit

  Streamlit — A faster way to build and share data apps.

  Language:Python33.5k3124.3k2.9k

• NVIDIA/DeepLearningExamples

  State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.

  Language:Jupyter Notebook13k3018243.1k

• academicpages/academicpages.github.io

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

  Language:JavaScript11.1k8934340.3k

• jldbc/pybaseball

  Pull current and historical baseball statistics using Python (Statcast, Baseball Reference, FanGraphs)

  Language:Python1.2k72210324

• pachterlab/gget

  🧬 gget enables efficient querying of genomic reference databases

  Language:Python896116371

• marbl/CHM13

  The complete sequence of a human genome

  887669397

• mikelove/awesome-multi-omics

  List of software packages for multi-omics analysis

  691546159

• fritzsedlazeck/Sniffles

  Structural variation caller using third generation sequencing

  Language:Python5302746788

• etal/cnvkit

  Copy number variant detection from targeted DNA sequencing

  Language:Python50631747164

• pyranges/pyranges

  Performant Pythonic GenomicRanges

  Language:Python4271221846

• pachterlab/BI-BE-CS-183-2023

  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

  Language:Jupyter Notebook3869360

• fritzsedlazeck/SURVIVOR

  Toolset for SV simulation, comparison and filtering

  Language:C++3371220346

• Boyle-Lab/Blacklist

  Application for making ENCODE Blacklists

  Language:C++25373834

• GFA-spec/GFA-spec

  Graphical Fragment Assembly (GFA) Format Specification

  Language:Makefile189327242

• hartwigmedical/hmftools

  Various algorithms for analysing genomics data

  Language:Java1812044056

• lh3/cgranges

  A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

  Language:C163111018

• virajbdeshpande/AmpliconArchitect

  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

  Language:Python1311110842

• GooglingTheCancerGenome/sv-callers

  Snakemake-based workflow for detecting structural variants in genomic data

  Language:Python7347534

• namphuon/ViFi

  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.

  Language:Python2742618

• nf-core/circdna

  Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

  Language:Python251532214

• dozmorovlab/excluderanges

  Genomic coordinates of problematic genomic regions as GRanges

  Language:R21232

• FadyMohareb/mapoptics

  MapOptics is a lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments.

  Language:Java16225

• chezbob/chezbob

  Language:JavaScript1363511

• sara-javadzadeh/FastViFi

  Detect viral infection and integration sites on NGS input. Manuscript is in preparation.

  Language:Python9192

• GavinHaLab/Griffin

  A flexible framework for nucleosome profiling of cell-free DNA

  Language:Python6104

• AmpliconSuite/AmpliconSuiteAggregator

  Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org

  Language:Python24

• AmpliconSuite/AmpliconRepository

  Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.

  Language:JavaScript141525

• genepattern/AmpliconSuite

  Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

  Language:Python1201