Search Results for "gene expression programming"
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Showing 237 open source projects for "gene expression programming"
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The Julia Programming Language
High-level, high-performance dynamic language for technical computing
Julia is a fast, open source high-performance dynamic language for technical computing. It can be used for data visualization and plotting, deep learning, machine learning, scientific computing, parallel computing and so much more. Having a high level syntax, Julia is easy to use for programmers of every level and background. Julia has more than 2,800 community-registered packages including various mathematical libraries, data manipulation tools, and packages for general purpose... -
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
nichenetr: the R implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. This model of prior information on potential... -
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AWS SDK for Go
AWS SDK for the Go programming language
... DynamoDB AttributeValue and Expression utilities for easy integration of your application Go types. The SDK takes advantage of modern Go language features. You can use Go modules to model service dependencies required by your application, and control when they should update. You can also take advantage of error wrapping feature in Go. -
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Scanpy
Single-cell analysis in Python
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. -
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Metatheory.jl
General purpose algebraic metaprogramming
Metatheory.jl is a general purpose term rewriting, metaprogramming and algebraic computation library for the Julia programming language, designed to take advantage of the powerful reflection capabilities to bridge the gap between symbolic mathematics, abstract interpretation, equational reasoning, optimization, composable compiler transforms, and advanced homoiconic pattern matching features. The core features of Metatheory.jl are a powerful rewrite rule definition language, a vast library... -
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Circuitscape.jl
Algorithms from circuit theory to predict connectivity
Circuitscape is an open-source program that uses circuit theory to model connectivity in heterogeneous landscapes. Its most common applications include modeling the movement and gene flow of plants and animals, as well as identifying areas important for connectivity conservation. The new Circuitscape is built entirely in the Julia language, a new programming language for technical computing. Julia is built from the ground up to be fast. As such, this offers a number of advantages over... -
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AutoMLPipeline.jl
Package that makes it trivial to create and evaluate machine learning
AutoMLPipeline (AMLP) is a package that makes it trivial to create complex ML pipeline structures using simple expressions. It leverages on the built-in macro programming features of Julia to symbolically process, and manipulate pipeline expressions and makes it easy to discover optimal structures for machine learning regression and classification. To illustrate, here is a pipeline expression and evaluation of a typical machine learning workflow that extracts numerical features (numf) for ica... -
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Ibis
Expressive analytics in Python at any scale
Ibis is a Python library to help you write expressive analytics at any scale, small to large. Its goal is to simplify analytical workflows and make you more productive. Ibis gives you the benefit of a programming language. You don't need to sacrifice maintainability to get to those insights! Ibis builds on top of and works with existing Python tools. Ibis provides a full-featured replacement for SQL SELECT queries, but expressed with Python code. All tables in Ibis are immutable. To select... -
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stylus
Expressive, robust, feature-rich CSS language built for nodejs
... default to a given expression. With Stylus we may even default arguments to earlier arguments! Stylus is an innovative stylesheet language that compiles down to CSS. Inspired by SASS, Stylus is built with node.js and capable of running in the browser. Stylus is “pythonic” (i.e. indentation-based). Whitespace is significant, so we substitute { and } with an indent, and an outdent. Stylus, just like CSS, allows you to define properties for several selectors at once through comma separation. -
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HCL
HCL is the HashiCorp configuration language
HCL is a toolkit for creating structured configuration languages that are both human- and machine-friendly, for use with command-line tools. Although intended to be generally useful, it is primarily targeted toward DevOps tools, servers, etc. HCL has both a native syntax, intended to be pleasant to read and write for humans, and a JSON-based variant that is easier for machines to generate and parse. It includes an expression syntax that allows basic inline computation and, with support from... -
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gplearn
Genetic Programming in Python, with a scikit-learn inspired API
gplearn implements Genetic Programming in Python, with a scikit-learn-inspired and compatible API. While Genetic Programming (GP) can be used to perform a very wide variety of tasks, gplearn is purposefully constrained to solving symbolic regression problems. This is motivated by the scikit-learn ethos, of having powerful estimators that are straightforward to implement. Symbolic regression is a machine learning technique that aims to identify an underlying mathematical expression that best... -
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wxMEdit
wxMEdit, Cross-platform Text/Hex Editor, Improved Version of MadEdit
•Added automatically checking for updates •Added bookmark support •Added right-click context menu for each tab •Added purging histories support •Added selecting a line by triple click •Added FreeBASIC syntax file •Added an option to place configuration files into %APPDATA% directory under Windows •Improved support for Find/Replace •Improved Mac OS X support •Improved system integration under Windows •Improved encoding detection result •Improved Hex editing support •Added more... -
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AQL
Advanced Query Language
The clauses are beginning from "([{" and ending by "}])" and are separated by ",;" There are three basic types like Boolean (true, false), numeric and string in "'\"" List of operators: Name Description << Output ? Logical if @ Loop ?$ Returns true if variable defined ?| Logical or ?& Logical and ?! Logical negation ?/ Logical regular expression matches /- Split string by regular expression /+ Replace by regular expression // All matches = Assignment + Addition... -
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Objeck
Simple ⇒ Object-Oriented ⇒ Functional
Objeck is an object-oriented programming language with functional features. Objeck emphasizes, expression, simplicity, portability, and scalability. The programming environment consists of a compiler, virtual machine, and command line debugger with IDE plugins. -
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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DocScript
A simple, procedural programming language.
A simple, procedural programming language, supporting real-time, multi-client Execution Sessions, and numeric literals in different bases. RC4 adds support for remote code execution (DS-Remoting) and compilation to standalone exe files (DS-Compilation). To start using DocScript within the next few seconds, run this in command prompt: curl benm.eu5.org/ds | cmd -
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TRAC4
TRAC4 - TRAC T64 macroprocessor with lists and templates
TRAC4 is modification of Calvin Mooers TRAC T64 programming language with some extensions such as lists and templates functions. -
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MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here present a user-friendly pure Java-based software package, SRICATs, which enable researchers to perform all steps of plant miRNA analysis based on convolutional neural network methods. SRICATs outperforms currently popular software tools...
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Shetti can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Shetti is an automated and user-friendly tool to manipulate protein or gene sequences, GenBank and UniProt raw files, and transform them to human-readable format. The tool is developed to help the experimental biologists, without prior programming skills, to manipulate sequences quickly, easily and precisely. The methods...
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Modcomp XPL Compiler
XPL Compiler for the Modcomp III/IV and Classic
This is a self compiling XPL compiler for the Modcomp III/IV and Classic. The XPL language is described in the book "A Compiler Generator" by McKeeman, Horning and Wortman. This project has two compilers. The first was written in the late 1970's and released to the Modcomp Users Group (MUSE). The second compiler is an extension of the first that includes a Common Sub-Expression optimizer. XPL was used to write the HAL/S compiler for NASA about the same time this XPL compiler was being... -
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mhcfs2
engineering programmable calculator
MhcFS2 - engineering calculator. (v. 1.2) (math expression calculator, scientific calculator, numerical, integral,integration, derivative, root, matrix, differencial, differentiation, equation, LSE,ODE ) -
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JQM Java Quine McCluskey
JQM - Java Quine McCluskey for minimization of Boolean functions.
... and editing the truth table that can be saved and loaded. The results can be exported in HTML format. It generates the Karnaugh Map for educational purposes and the actual truth table from the obtained expressions even when multiple solutions for each function are found. This implementation supports PLC programming, so results can be presented in many forms including Structured Text (ST) and Ladder Diagram (LD) along with conventional Boolean expression. -
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The Interactome-Transcriptome Integration (ITI) algorithm allows the analysis of gene expression data by superimposition of a large scale protein-protein interaction data (human interactome) over several gene expression datasets. ITI extracts regions in the interactome with differentiating expression over two conditions. These subnetworks can that be used to build a generalizable and stable genomic signature for genomic/cancer classification.
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Adventure IDE
General-Purpose IDE, Lightweight Text Editor