Search Results for "bioinformatics linux" - Page 2
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Showing 323 open source projects for "bioinformatics linux"
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Despite the substantial progress facilitated by bioinformatics tool development, some of them are tailored for specific analytical objectives and code-based, and challenges arise when non-bioinformaticians users need to integrate the outputs of these specific tools into a personalized and appropriate pipeline for their research demands. To address this, we developed BioPipeline Creator, a user-friendly Java-based GUI for managing and customizing biological data pipelines according to...
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Please, do not hesitate to contact us if you need help. https://sites.google.com/view/hsa23/ Short linear motifs / domains (SLiM) facilitate the functions and interactions of the proteins. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. ShettiMotif, which is an interactive tool to (i) searches for motifs containing repeated residues (e.g. Leu-, SR-, PEST-rich motifs, etc.), (ii) searches for multiple...
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. 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... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw,... -
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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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GenTreat is a computational pipeline with an intuitive graphical interface, was developed for automated hybrid assembly of prokaryotic genomes, performs assembly using two assemblers, merges the results, and then orders and annotates the assembled genome. Validation using raw reads from 61 organisms demonstrated that is a viable alternative for automated hybrid assembly, eliminating the need for using extensive command lines.
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J-Circos
J-Circos: An Interactive Circos plotter
J-Circos is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. j.an@qut.edu.au please cite An J, Lai J, Sajjanhar A, Batra J, Wang C, et al. J-Circos: an interactive Circos plotter. Bioinformatics. 2015;31:1463–5 -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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scDAPA
Detection and visualization of dynamic alternative polyadenylation
scDAPA - a tool for detection and visualization of dynamic alternative polyadenylation from scRNA-seq data [1] scDAPA user manual Please visit the Wiki page of this website. [2] scDAPA Q&A For Q&A, please visit the Blog page of this website. [3] scDAPA bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite scDAPA? Ye C, Zhou Q, Wu X, Yu C, Saban D.R, Li Q.Q (2020) scDAPA: detection... -
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA... -
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Allelome.PRO
A pipeline to define allele-specific genomic features
Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively... -
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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
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. 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... -
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AmPEP and AxPEP
Sequence-based Antimicrobial Peptide Prediction by Random Forest
Antimicrobial peptides (AMPs) are promising candidates in the fight against multidrug-resistant pathogens due to its broad range of activities and low toxicity. However, identification of AMPs through wet-lab experiment is still expensive and time consuming. AmPEP is an accurate computational method for AMP prediction using the random forest algorithm. The prediction model is based on the distribution patterns of amino acid properties along the sequence. Our optimal model, AmPEP with 1:3... -
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corona
Reverse engineering SARS-CoV-2
corona is an exploratory bioinformatics project that applies reverse-engineering ideas to SARS-CoV-2. It treats biological information processing as an analogy to software analysis to help explain the viral genome from first principles. Python scripts download genomic sequences from GenBank and translate RNA into amino-acid chains. The project identifies and annotates proteins encoded by the genome. It also experiments with OpenMM for molecular simulation and protein-folding work. Supporting... -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome... -
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parallelblast_plus
Database sliced Blast implementation
Updated versions of programs described in: Parallel BLAST on split databases" Bioinformatics 2003 Sep 22;19(14):1865-6. https://doi.org/10.1093/bioinformatics/btg250 but which now work with modern BLAST versions. -
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AGELESS
Software for systematic study of Parents and their hybrids
NGS technology although has its obvious advantages, poses serious bioinformatics challenges in analyzing and extracting meaningful information. Plenty of tools have been developed for the analysis of NGS data that are mostly catered towards diploid genomes. Despite such a rich tool set, it is difficult to improvise and use them on genomes which are aneuploid. We were also handicapped by the lack of suitable analytical pipeline that allows studying the experimental hybrids systematically. We... -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH... -
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PyArmadillo
linear algebra library for Python
PyArmadillo - streamlined linear algebra library for Python, with emphasis on ease of use. Alternative to NumPy / SciPy. * Main page: https://pyarma.sourceforge.io * Documentation: https://pyarma.sourceforge.io/docs.html * Bug reports: https://pyarma.sourceforge.io/faq.html * Git repo: https://gitlab.com/jason-rumengan/pyarma -
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Palibino
Pascal library for bioinformatics
Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology. -
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APAtrap
Identification of APA sites from RNA-seq data
APAtrap - a tool for identification of APA sites from RNA-seq data. [1] APAtrap user manual Please visit the Wiki page of this website. [2] APAtrap Q&A For Q&A, please visit the Blog page of this website. [3] APAtrap bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite APAtrap? Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative... -
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
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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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DeepLearning
Deep Learning (Flower Book) mathematical derivation
" Deep Learning " is the only comprehensive book in the field of deep learning. The full name is also called the Deep Learning AI Bible (Deep Learning) . It is edited by three world-renowned experts, Ian Goodfellow, Yoshua Bengio, and Aaron Courville. Includes linear algebra, probability theory, information theory, numerical optimization, and related content in machine learning. At the same time, it also introduces deep learning techniques used by practitioners in the industry, including...
