Search Results for "python data analysis" - Page 125
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Showing 6383 open source projects for "python data analysis"
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
jChIP is a GUI-based Java application for ChIP-Seq data analysis. It was created to build binding profiles between proteins and loci in the genome. In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676 -
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Garmin Connect Python Uploader
A python script to upload .tcx, .fit, and .gpx files to Garmin Connect
This project, gcpuploader, helps you to upload files created by your Garmin fitness GPS (.tcx, .fit, or .gpx files) to the Garmin Connect web site (connect.garmin.com) once they are extracted from the device. It was developed because of Garmin's utter lack of support for Linux OS. This Python project has been tested in a limited capacity in Python 2.6.5 under Linux and Python 2.7.2 under Windows XP as well. **Tapiriik is an open source web service which syncs data between various sports... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
... are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a -
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MicrobeGPS
The Explorative Taxonomic Profiling Tool for Metagenomic Data
MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily. -
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PyPago
Python Physical Analysis of the Gridded Ocean
This set of programs aim at diagnosing gridded ocean models of any kind along pre-defined sections and closed volumes. -
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pipasic
pipasic: Protein Abundance Correction in Metaproteomic Data
Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising... -
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PhyloPipe
PhyloPipe is a combination of some polular phylogenetic software
Bioinformatics is a promising interdisciplinary, designed to use a computer to handle large and complex biological data, aiming at revealing the hidden mysteries of biology. Analysis of the evolutionary biology, one of the main branches of bioinformatics, uses several common software such as HaMStR,MUSCLE, RaxML. Running different procedures successively, we can get the evolutionary analysis eventually. Since the input and output data between different software are not always compatible... -
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chipexo
model based analysis of ChIP-exo data
Here we developed a novel analysis framework named MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. When applied to yeast Reb1 and human CTCF ChIP-exo data, MACE is able to define TFBSs... -
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MZmine 2
A framework for differential analysis of mass spectrometry data
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data. -
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Web-TCGA
A light weight tool to access TCGA data
The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. Therefore we created Web-TCGA, a web based, freely accessible online tool, for integrated analysis of molecular cancer data sets, provided by the TCGA. In contrast to already available tools, Web-TCGA utilizes different methods... -
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snakeFlow - collector for flow protocol version 5 writetten on python 2.7 By default output data to the console. May store file data and the database MySQL docs (2 parts): http://snakeproject.ru/rubric/article.php?art=python_netflow_collector_1 http://snakeproject.ru/rubric/article.php?art=python_netflow_collector_2
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GASiC
Genome Abundance Similarity Correction
One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed... -
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SCaVis
Scientific Computation and Visualization Environment
SCaVis is an environment for scientific computation, data analysis and data visualization for scientists, engineers and students. The program is fully multiplatform (100% Java) and integrated with Java and a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. SCaVis can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations... -
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bnmroffice
Beta version of bnmroffice v2
The program is used for bNMR data analysis. To download the latest version, please follow the link https://github.com/hsaadaoui -
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Natural Language Analysis with Ngrams
NLP tool for statistical analysis of words, sentences, documents
Goal of this project is to have a NLP tool that would give statistical analysis results based on Google Ngram data. Furthermore, it is now just a NetBeans project without a final JAR. Furthermore, there will be a github version for anyone who wishes to contribute. In the future versions, user will be able to convert a single word to numerical data, to be able to compare two words and get the comparison data, and to be able to do the same for the sentences, paragraphs and documents. I... -
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Community Linux
USB Drive Writable Linux Distribution
Community Linux is a USB drive based fully functional writable Linux Distribution. It boots and runs with a comparable speed as a hard drive installation. Community Linux allows one to create a low cost solid state development and production platform. For new ComLin drive creation, one needs to download the full install (comlin-016.tar.gz) ... (not just the scripts) Update: Community Linux will now run on most every machine. Update: Added Sound drivers, Intelligent... -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW....
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qtFit is a program used to fit ASCII data. The graphical user interface (GUI) of qtFit is designed using QT software. The regression is done using CERN’s MINUIT routine and plotting is perfomed with the QCustomPlot library. This document is a manual of the qtFit program, and includes instructions about installation, features description, and how-to-use examples.
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irit_diff_sequences
Python tool to create lifespan sequences from Wikipedia edits history
A Python tool which produced lifespan sequences from edits history. The tool is first developed for the Wikipedia edits history but can easily be adapted for others applications. From a database containing for each article its list of revisions, produce one csv file per article containing authored sequences and lifespans. Output format: i,j,lifespan,author with - i : begining of the chars sequence - j : end of the chars sequence - lifespan : number of edits the sequence has survives... -
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Larch: Data Analysis for X-ray Spectra
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. Larch... -
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bayescount
The bayescount R package
A set of functions to allow analysis of count data (such as faecal egg count data) using Bayesian MCMC methods. Returns information on the possible values for mean count, coefficient of variation and zero inflation (true prevalence) present in the data. A complete faecal egg count reduction test (FECRT) model is implemented, which returns inference on the true efficacy of the drug from the pre- and post-treatment data provided, using non-parametric bootstrapping as well as using Bayesian MCMC... -
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ospfdiscoverysnmp
OSPF network discovery script via SNMP.
... between his PC and the router into the OSPF process, so he has IP connectivity to all other OSPF nodes. After providing necessary info and the OSPF info is gathered, the user has three choices: display the OSPF routers info on the screen, export the data to a file for Excel importing and generate the OSPF topology showing neighborships, router IDs and neighbor IPs. Tools used for coding and testing: Python 2.7.3, PySNMP, GNS3, Linux. Tested on Cisco 2621, 2691, 3660. -
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*WARNING* gtburst moved to github (https://github.com/giacomov/gtburst). ########################################## gtBurst is a tool to download data, analyze and simulate Gamma-ray Bursts and Solar Flares as observed by the NASA Fermi satellite.
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2bRAD-GATK
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
...; - base quality score recalibration; - calling variants; - variant quality score recalibration based on genotyping replicates; - smart-thinning and final filtering; - quality assessment based on replicates. also included are walkthroughs for analysis: - generating data for genome scans (Fst, BayeScan, pi, Tajima's D, deviations in Linkage Disequilibrium) - ADMIXTURE -
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PhenoSim3D
Virtual Physics Laboratory - PhenoSim3D
PhenoSim3D is an application that presents computer simulations of real physical experiments, which could be used for demonstrating laws and effects in the field of Physics. Unlike real experiments, the simulations with PhenoSim3D could be done in a time convenient for the user; in addition, the greater data precision makes the phenomena analysis understandable, and due to the lack of external factors PhenoSim3D allows for repetition of the experiments without changes in the results...
