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Showing 75 open source projects for "suite"
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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...The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite
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PsPM
A matlab suite for Psycho-Physiological Modelling
PsPM is a powerful tool for psychophysiological modelling. It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although... -
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The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
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Root Phenotyping Suite
Three different software tools for phenotyping plant root images
RootAnalyzer is a fully automated tool, for efficiently extracting and analyzing anatomical traits from root-cross section images. RootAnalyzer segments the plant root from the image's background, classifies and characterizes the cortex, stele, endodermis and metaxylem, and produces statistics about the morphological properties of the root cells and tissues. RTipC is a system for the fully automated detection and classification of root tips in root images obtained either by 2d flat bed... -
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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fourSig
Analyze 4C-seq data.
fourSig is a suite of programs for analyzing and visualizing 4C-seq data. -
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CSBB-v2.0
Computational Suite for Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. -
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please... -
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Community Detection Modularity Suite
Suite of community detection algorithms based on Modularity
...Ball et al, An efficient and principled method for detecting communities in networks, 2011. The suite is based upon the fast community algorithm implemented by Aaron Clauset <aaron@cs.unm.edu>, Chris Moore, Mark Newman, and the R IGraph library Copyright (C) 2007 Gabor Csardi <csardi@rmki.kfki.hu>. It also makes of the classes available from Numerical Recipies 3rd Edition W. Press, S. Teukolsky, W. Vetterling, B. Flanne -
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Suite of tools for DNA sequence analysis - searching (EST, mRNA, sequencer reads); aligning (ESTs, mRNA, whole genome); and analysis (repeats, kmers).
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SHORE is a Next Generation Sequencing data analysis suite. Please find the manual at http://shore.sourceforge.net/wiki
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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 multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. ... -
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riboshape
Predicting ribosome footprint profile shapes from transcript sequences
Riboshape is a suite of algorithms to predict ribosome footprint profile shapes from transcript sequences. It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. -
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MULTOVL
Multiple overlaps of genomic regions
The MULTOVL suite of programs finds multiple overlaps among genomic regions. The MULTOVL algorithm can detect several kinds of region overlaps. In addition to the N-fold overlaps you can detect solitary regions which are the input regions that do not overlap with any other region in the input data set, and union overlaps that is the union of the input regions that overlap at least once somewhere. -
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...HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. ...
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MORPHE
MORphological PHenotype Extraction
MORphological PHenotype Extraction (MORPHE) is a suite of automated image processing, visualization, and classification algorithms to facilitate the analysis of heritable and clonal red-to-green transitions that occurred during the growth of a colony. -
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Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data.
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The Genome Mappability Analysis suite is used for measuring how well NGS reads can be mapped to reference genomes, especially for discovering variations