Search Results for "sample"
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Showing 41 open source projects for "sample"
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WxTools (Weather Data Tools)
This package collects Fine Offset and Oregon Scientific weather data.
...The software works with the Fine Offset WH290 and similar models (including clones such as the Pro-Signal PSG04173). It also works with the Oregon Scientific WMR180 weather station (and probably similar models such as the WMR88 and WMR100) as well as the older WMR928. Sample weather data is provided. -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not... -
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LiVES
LiVES is a Video Editing System. It is designed to be simple to use, y
...You can even record your performance in real time, and then edit it further or render it straight away. For the more technically minded, the application is frame and sample accurate, and it can be controlled remotely or scripted for use as a video server. And it supports all of the latest free standards. -
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lm-sensors
lm-sensors repository
lm-sensors is the canonical Linux project for reading motherboard and peripheral hardware sensors—temperatures, fan speeds, voltages—and exposing them to userspace. It ships a probing utility (sensors-detect) that identifies I²C/SMBus chips and kernel drivers, then a runtime tool (sensors) that prints human-readable readings for quick diagnostics. The companion library, libsensors, gives applications a stable API to query sensor values, enabling desktop applets, monitoring daemons, and... -
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bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
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Accent Tool Suite
Accent interfaces and controls systems through goals and policies
Accent (Advanced Component Control Enhancing Network Technologies) is a comprehensive tool suite that interfaces a variety of communications systems and allows these systems to be controlled through goals (high-level user aims) and policies (lower-level system rules). Accent has been applied to the domains of: o Call Control: for telecommunications, particularly call control in Internet telephony o Home Care: for home automation and telecare, particularly for domestic appliances... -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. ... -
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. ... -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining. -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
11
NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
...If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313. -
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ecw2sfz
Convert Ensoniq .ECW files to .SFZ
".ECW file" or "waveset" refers to a file with an extension of ".ECW" which stores articulation and sample data used by the MIDI synthesizer of sound cards equipped with an ES1370, ES1371, or ES1373 chip. These sound cards include the Ensoniq AudioPCI, the Sound Blaster! AudioPCI, the Sound Blaster! PCI64, the Sound Blaster! PCI128, and the Sound Blaster Live!. This project is a Perl script which can unpack these files into a .WAV sample, and a corresponding .SFZ file (an open format used by various sample engines to describe sample playback.) -
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MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
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Automalator
State Dependency deconstructor and mapper for C source code.
Flowcharts not telling you what you want to know about some C source code? Try a State Dependency map! Every C source file is an implemention of a state machine. Implicit in the definition of a state machine is a network of dependencies between the states. The Automalator * deconstructs the C code into the core state machine * collates the transactions into the dependency net * generates a diagram-format file with the states and dependencies as the nodes and edges. ... -
15
Caplan Capacity Planning
Unix capacity planning tool
This tool will try to be a capacity planning tool. A demo of the SVN version is available at http://zelionix.ddns.net/ It make plots from KPI ( CPU , Memory, Volume ) collected by an agent. Warning and critical levels are toogled by night collecte, load, analyse treatment This tool is designed to check your infrastructure capacity and challenge it against your capacity planning. The project contain a Server - Front-end web based - Back-end with a night job for data collect... -
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
...We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated individuals, given a specified threshold of relatedness. Additional information for preferential selection of individuals may also be utilized. For example, when there are two equally sized maximum sets of unrelated individuals in a network, PRIMUS can preferentially select the set with more affected individuals. ... -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting... -
18
MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads. -
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SportsCameraOverlay
Overlay GPS info on videos taken with a sports camera
...This way the program can be used for overlaying GPS info onto any brand of sports camera. Currently two overlay types are available, a "speedo" overlay and a "digital" (textual) overlay designed around snowsports. A few sample videos: http://www.youtube.com/watch?v=RHWcOntLT5Q http://www.youtube.com/watch?v=HelsKZeIRlM Note: This project is in its infancy and will only work on linux based operating systems without significant code changes. -
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Linux Exploit Suggester
Linux Exploit Suggester; based on operating system release number
...The tool intentionally keeps its logic simple: it performs string matching and warns that patched or back-ported kernels can mislead results, so its output should be treated as pointers for further verification rather than definitive proof of exploitable code. Sample output demonstrates common exploit names, CVEs, and direct exploit-db / vendor links to aid triage. -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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CAPE RNA
Classification based Analysis of Paired Expression data of RNA
CAPE RNA is package of command-line tools for integrated analysis of miRNA-mRNA expression data. miRNA-mRNA interaction states are assigned for each sample independent of a priori known experimental groups. Using these interaction classifications Jaccard-indexes are calculated to evaluate the quality of a predicted interaction based on the distribution of assigned interaction states compared to experimental groups. In addition, negative correlation between miRNA and mRNA expression can be analyzed. -
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ALSA MIDI Filter (AMF)
A MIDI filter that uses the ALSA MIDI libraries
The ALSA MIDI filter application runs as an ALSA MIDI client that can receive input from a source (such as a sound card hooked up to a MIDI keyboard), perform various filtering and other functionality based on the type and content of the MIDI input, and send the result to one or more other MIDI clients. -
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A pipeline to revise a genome sequence of a prokaryotic sample via an iterative backbone remapping and local assembly method.
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BrutefirDRC
Apply digital room correction and/or loudness to LogitechMediaServer
A plugin to use the BruteFIR software convolution engine with slimdevices SqueezeCenter clients for Digitial Room Correction. Provides transparent/automatic switching of filters for different sample rates. Filter creation can be done with DRC, Audiolense, acourate or other DRC-software. An optional loudness correction using the digital volume control can be applied. The loudness features uses sox loundess that is based on the ISO 226 curves.
