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Java based workflow generator to deploy WES variant detection pipelines on Kubernetes using Argo. Reads WDL files and produces Argo compatible work flows specifciying compute cluster environment (pod) on which the workflow component should be executed and the buckets in which the results should be dropped
Gives most probable and least probable DNA Sequences for input protein sequence
Simulation of baseline survey response variables to store information in EPIC Number of variables: 495 Code: Java 8 Reads in csv file of variables and value range of permitted responses Use randomization to a) induce error b) generate valid responses, and simulate 1M responses, to use as prototype data to populate i2b2 deployments in support of the MVP project for VABHS
ETL scripts to populate caBIO database
perl script that reads file in multifasta format and complements it
ETL scripts to populate caMOD database with MTB data from Jackson Labs
Code that polls beckman coulter and stores rack information, and protocols initiated (if any) on samples.
Converts DNA to Protein along 1, 6 (fwd or reverse strand) or user defined frames
1st Edition of Elegant SciPy (O'Reilly Publishers)
Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, per tile sequence quality
C++ code to calculate nmer frequencies (n= 1 to 6) and write out to file
Finds palindromes and inverted repeats in DNA Sequences based on user defined inputs
Interface to Biomek that performs 1D and 2D Scan of aliquots (2d) and rack (1d) ; reads freezer configuration from DB and assigns location to plate
Python package to parse GATK Output and extract summary statistics at mbq 0,10,20,30 and variant evaluation metrics
Java based implementation of an MLE method using chi square test to calculate interference during meiotic crossover (the number of double strand dna breaks that don't result in a crossover)
Kmer counter is written in GO Lang v 1.16.5 To install GO on Windows, follow the instructions at https://golang.org/doc/install 4 GO implementation of N-mer counter in DNA sequences which tests for validity of input. It reads in file name (of fasta file) It reads the size length (kmer length) for which counts are desired and writes out to file, counts of all overlapping kmers of size 1 through the specified input. It checks if fasta file is empty amd whether kmer length is specified.
Module for tracking tubes and aliquots and assign storage in the freezers ; Part of the MVP specimen processing system VABHS. Prototype
Microarray data analysis using R / BioConductor
Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5
Wrapper script that calls formatdb on nr database and then runs blastall against formatted db and parses the output.
16sRNA Microbial Profiling R scripts to find most significant OTUs in 16RNA data after data normalization, followed by ordination and clustering and then plotting iTOL
Variant caller from pileup notation / samtools alignment
Takes as input FNA file, PTT file, desired probe length, cross-reactivity allowed, overhang
restriction enzyme cleavage site identifier using kmp algorithm and REBASE
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.