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Showing 27 open source projects for "utf-8"
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XLibraryDisplay
A sequence analysis tool for protein engineering
...It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
...Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
...It uses RNAfold to predict sequence structure and UShuffle to generate random sequences with a defined k nucleotide frequency. Also, sequences in GenBank format can be downloaded directly from NCBI using the NCBI access ID. Requirements JAVA Runtime 8. It's highly recommended to have a multicore processor to process large sequences. * Currently, this version only runs in Windows x64. -
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TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
...More detailed information on TCellXTalk and the people at the CSIC/UAB Proteomics Laboratory behind it can be obtained at https://www.tcellxtalk.org/about/ - Casanovas, A., Gallardo, Ó., Carrascal, M., Abian, J., TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics 2019, 35-8, 1404–1413, DOI 10.1093/bioinformatics/bty805 ( https://doi.org/10.1093/bioinformatics/bty805 ) -
AI-powered service management for IT and enterprise teamsGive your IT, operations, and business teams the ability to deliver exceptional services—without the complexity. Maximize operational efficiency with refreshingly simple, AI-powered Freshservice.
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TIES
A smart search engine for medical documents
...It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer maintained, as of 8/15/2019. You are free to continue to use this software under the license for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com -
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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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CognitionMaster
object-based image analysis framework
Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34 -
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spectralHMM
A spectral method for inferring selection from time series data
...This software implements the algorithms described in the following paper: Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222 -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
...Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data. -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data.... -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
...MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result). The program provide a step praramter (8 steps) which can allow running program from any step and finishing all remaining steps. You also can run step by step using each step program. Please run these step programs at the same directory for running main program MITP.pl. Some steps are optional (read filter, expression, miRNA class and target). When you select the related parameters belong to these optional steps, the program will run these steps. ... -
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fast_count_multi
Extremely fast NGS read counter
Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. -
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MCCCS
Multi Channel Classification and Clustering
Here we present an image-based Multi Channel Classification and Clustering System (MCCCS). It is an generalized, script-based classification system for processing various kinds of image data. Due to the modular design, individual processing-components can be easily adapted, extended or exchanged by own extensions. See project website for installation instructions. -
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SoftSV
Calling structural variations. The soft way.
...For more information about the algorithm and an evaluation, have a look at this publication: "Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms" (PMID 25998133) Please cite this artilce if you used SoftSV in your publication. -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
...SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632 -
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...For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out (August 2013): http://mbe.oxfordjournals.org/content/30/8.toc. For the multimodel version of CodonPhyML, please use the 'codonphyml_multi.tgz' tarball.
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SyntheticWSI
Tools to generate and visualize artificial whole slide images
Java 8+ required. Collection of tools to help generate artificial Whole Slide Images (WSIs). A WSI is stored as a ZIP archive of JPG tiles, and this software contains a tool to visualize this format. SVS files can be used directly for texture extraction (thanks to the included Bio-Formats library). Main source files in package fr.unistra.wsi.synthetic. -
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CS Miner
A tool for Navigating in Chemical Space
...It helps for deriving appropriate classification models and performing virtual screening. Download it via: http://csminer.com/csm/?p=7 A quick tutorial is available through: http://csminer.com/csm/?p=8 -
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...MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). References: 1. M. Rho et al., "De novo identification of LTR retrotransposons in eukaryotic genomes", BMC Genomics (2007) 8:90. 2. M. Rho and H. Tang, "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes", Nucleic Acids Research (2009) 37:21.
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GOFG Sports Computer
Free GPS tracking software for your workouts.
...The most important features are: - GPS tracking of your training - upload workouts to gofg.at and share them using twitter and facebook - analyze your exercises using a map-display & altitude graph - keep track of various statistics like ODO-meter - ships with English, German, Italian and Spanish user interface - export to Fitlog, TCX and GPX Currently Android, iOS and Windows Phone 7 & 8 are supported. -
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...Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
.... ******************************************************************************************************************************** PROJECT MIGRATED TO GITHUB FOR FUTURE UPDATES: https://github.com/biocoder/SBEToolbox/releases ******************************************************************************************************************************** Reference ( In Press ): ================= Konganti K, Wang G, Yang E, Cai JJ* (2013). SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 8:1-15 -
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MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
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A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
