Pinned Repositories
adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
Augustus
Genome annotation with AUGUSTUS
bamtools
C++ API & command-line toolkit for working with BAM data
BaseSpace_Clarity_LIMS
API libraries, application examples, and custom tools for BaseSpace Clarity LIMS
bedtools2
A powerful toolset for genome arithmetic.
bfx-qc-reporter
Bioinformatics QC Reporting Tools
bioawk
BWK awk modified for biological data
bstring
A fork of Paul Hsieh's Better String Library
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
ClinicalDataSources
Open or Easy Access Clinical Data Sources for Biomedical Research
basesLoaded's Repositories
basesLoaded/adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
basesLoaded/Augustus
Genome annotation with AUGUSTUS
basesLoaded/BaseSpace_Clarity_LIMS
API libraries, application examples, and custom tools for BaseSpace Clarity LIMS
basesLoaded/bedtools2
A powerful toolset for genome arithmetic.
basesLoaded/cpython
The Python programming language
basesLoaded/deepTools
Tools to process and analyze deep sequencing data.
basesLoaded/fastai
The fast.ai deep learning library, lessons, and tutorials
basesLoaded/hibachi
Data simulation software that creates data sets with particular characteristics
basesLoaded/htslib
C library for high-throughput sequencing data formats
basesLoaded/interop
C++ Library to parse Illumina InterOp files
basesLoaded/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
basesLoaded/KAT
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
basesLoaded/MegaQC
Web application to collect and visualise data across multiple MultiQC runs.
basesLoaded/mothur
Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
basesLoaded/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
basesLoaded/NA12878
Data and analysis for NA12878 genome on nanopore
basesLoaded/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
basesLoaded/Pisces
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
basesLoaded/PrimateAI
deep residual neural network for classifying the pathogenicity of missense mutations.
basesLoaded/python-intro
Materials for the Peter Mac "Introduction to Solving Biological Problems with Python" 4 week course
basesLoaded/qiaseq-dna
example code for processing reads from QIAGEN QIAseq DNA enrichment kits
basesLoaded/qiaseq-smcounter-v2
basesLoaded/rtg-tools
RTG Tools: Utilities for accurate VCF comparison and manipulation
basesLoaded/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
basesLoaded/strelka
Strelka2 germline and somatic small variant caller
basesLoaded/stringtie
Transcript assembly and quantification for RNA-Seq
basesLoaded/tpot
A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
basesLoaded/vcfR
Tools to work with variant call format files
basesLoaded/vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
basesLoaded/ZingChart
A declarative, efficient, and simple JavaScript library for building responsive charts