Scripts and code pertaining to "Human microRNAs Exhibit Two Distributions Within and Across Cancer Samples" :cancer: Summarize, Analyze and Visualize MAF files from TCGA or in house studies.įast genome and metagenome distance estimation using MinHash Lumpy: a general probabilistic framework for structural variant discoveryĬonvert a maf file to a bed file to use with BEDtools. MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.Ī threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng LiĪ small python utility which can execute a list of commands in parallelĪn extensible C++ library of Hierarchical Bayesian clustering algorithms, such as Bayesian Gaussian mixture models, variational Dirichlet processes, Gaussian latent Dirichlet allocation and more.Ī small library for generating VCF headersĪ thread-safe LRU cache implementation in C++ The scripts and JSON descriptions necessary to run samtools mpileup on Stampede using iPlant The scripts and JSON description necessary to produce a working iPlant version of GATK Realignment/Recalibration.Ĭontains the necessary files to create a working version of Platypus on iPlant :beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managersĬontains scripts used to analyze HPV samples sequenced on ONT minIONs.įiles and scripts for generating a pan-genome reference graph for learning models.Ĭontains all of the bits and pieces needed to integrate BWA indexing into the iPlant environment. Tool to build a (Human) Genome Variation Map from a set of data sources Simulation scripts and other items for comparing SV callersĪdapter script to integrate AgBase GoAnna resource with iPlant DEĮfficient alignment of strings to partially ordered string graphs Graphical Fragment Assembly (GFA) Format Specification Standalone C library for assembling Illumina short reads in small regionsĭockerfiles and WDL descriptions for various tools on Broad FireCloudĪ collection of scripts for munging genomic and epigenetic data from the Broad Firehose.īayesian haplotype-based genetic polymorphism discovery and genotyping.Ī C++ library and utilities for manipulating the Graphical Fragment Assembly format. Reference bwa aln implementation for Agave APIĪ single molecule sequence assembler for genomes large and small.Ĭore calling tools in a convenient docker imageĭELLY2: Structural variant discovery by integrated paired-end and split-read analysisĪ python script/minimal GUI app for aggregating variant annotations and predicting impacts Tools, scripts and programs for playing with biological data I'm a graduate student building tools for analyzing complex datasets in genomics.Īffinity Propagation with Sparse SimilaritiesīASH logic for generating a coverage-reduced BAM fileĭockerfiles for several SV callers and other miscellaneous bio apps. Sanger Institute | National Cancer Institute
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