Search Results for "bioinformatics"
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Showing 94 open source projects for "bioinformatics"
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TomoJ
ImageJ plugin to perform Electron Tomography
...registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al -
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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AngClust
AngClust: Angle-based feature clustering for time series
Citation: Aimin Li, Siqi Xiong, Junhuai Li, Saurav Mallik, Yajun Liu, Rong Fei, Hongfang Zhou, Guangming Liu. AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles. January 2022. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. DOI: 10.1109/TCBB.2022.3192306 Full text: https://ieeexplore.ieee.org/document/9833353/ https://pubmed.ncbi.nlm.nih.gov/35853049/ Highlights * We proposed a novel clustering algorithm based on angular features for short-term gene expression profiles. * We defined three indicators to identify significant clusters: (i) the fluctuation degree of expression levels, (ii) homogeneity, and (iii) the degree of clustering while the clusters are functionally significant... -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
...User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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TASSEL
TASSEL is a bioinformatics software package
TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. -
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TSMiner is a software program for reconstructing time-specific regulatory networks for time-series expression data. TSMiner has three key modules: first, predicting the time-specific activated/repressed transcription factors (TFs); second, predicting the biological pathways associated with the predicted TFs; third, merging the TFs and pathways into time-specific regulatory networks. TSMiner provides extensive interactive operations to help users explore the results of each module. For...
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
...Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
LoopMatcher is a bioinformatics tool that searches for hairpin structures in cDNA / mRNA sequences (in FASTA, GenBank or Vienna format) with specific consensus sequences in the loop. 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. -
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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NOVA
Analysis and visualization of complexome profiling data.
...Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441 -
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Lirex
A Package for Identification of Long Inverted Repeats in Genomes
...Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. For more details, please refer to Genomics, Proteomics and Bioinformatics 2017, 15:141-146 by Y. Wang and J.M. Huang. -
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. ... -
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HSRA
Hadoop spliced read aligner for RNA-seq data
...RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. ... -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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GMOL
A tool for 3D genome structure visualization
...It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. ... -
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EntOpt Layout
Relative entropy optimization network layout plugin
...If you are using the plugin, please cite: Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks, Bioinformatics 35(21):4490-4492 https://academic.oup.com/bioinformatics/article/35/21/4490/5475596 Our detailed Tutorial on the use of the plugin: https://suopte.com/entopt_2_1_tutorial_20200518.pdf A video about the version 2.1: http://suopte.com/entopt_2_1_tutorial_video.mp4 Don't hesitate to send any questions, comments or bug reports also to agg.bence {at} med.semmelweis-univ.hu. -
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Citation: Sivakumar TV, Giri V, Park JH, Kim TY, Bhaduri A. ReactPRED: a tool to predict and analyze biochemical reactions Bioinformatics. 2016 Aug . pii: btw491.
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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
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BioDWH is a bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local RDBMS. It provides up-to-date integrated knowledge, platform and database independence.
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BABA stands for Basic-Algorithms-of-Bioinformatics Applet. This project aims to create a set of bioinformatic algorithms presented didactically. The algorithms available at the moment are: Needleman&Wunsch, Smith&Waterman, Four Russians and Nussinov.
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bioNerDS
Bioinformatics Named Entity Recogniser for Databases and Software
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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GESPA
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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Matchup
Bioinformatics tool for universal primers and group-specific probes
Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.
