Search Results for "all-in-one" - Page 3
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Showing 531 open source projects for "all-in-one"
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Red Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
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Paligo is an end-to-end Component Content Management System (CCMS) solution for technical documentation, policies and procedures, knowledge management, and more.
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
..., for each potential gene target it calculates an incidence matrix with all the miRNAs of each database targeting such gene. Finally, it builds a consensus matrix with the cases of the appearance of each miRNA in the four analyzed miRNA databases. -
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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. Requirements JAVA Runtime 8. It's highly recommended to have a multicore processor... -
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obo An umbrella organization for ontologies and structured shared controlled vocabularies for use across all biological and biomedical domains
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
... using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
Venn is a secure workspace for remote work that isolates and protects work from any personal use on the same computer. Work lives in a secure local enclave that is company controlled, where all data is encrypted and access is managed. Within the enclave – visually indicated by the Blue Border around these applications – business activity is walled off from anything that happens on the personal side. As a result, work and personal uses can now safely coexist on the same computer.
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub... -
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MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both...
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods... -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
.... After optimization, MAMA accurately simulated more than 87% of gene expression. See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22. -
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Corona Tracker
Coronavirus tracker app for iOS & macOS with maps & charts
Coronavirus tracker app for iOS & macOS with map & charts. https://coronatracker.samabox.com/ -
Deliver a personalized customer experience with every interaction, across every channel, with uContact, net2phone’s cloud contact center solution.
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HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one... -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports... -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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Peak List 2 MSP
Simple peak list to MSP file converter
Peak List 2 MSP takes your ascii mass/intensity pair list (or lists) and swaps them into MSP format (NIST standard text files for searching). It: takes lists from the clipboard (or drag and drop), sorts them by mass, normalises intensities, rejects below a cut off (that you define), adds MSP headers, puts the result back in the clipboard (or a file), has a command line interface so you can pass files in programmatically, has an api so you can... -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007...
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions... -
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bwfinder
Exogenous feature extractor from brainwaves
This program for Scilab searches for primary peaks in the segments of brainwave signal spectrum which are much above the signal spectrum average. Brainwave segments of 1 s are Fourier transformed, thresholded and merged if contiguous. Selected segments are drawn in time domain, frequency domain and a narrow-band analysis at 75 Hz is attempted. This program should detect strong external signals in brainwave recordings. Weak signals are not detected. This program requires the "edf2ascii... -
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JCVI VIGOR
Viral Genome ORF Reader
VIGOR (Viral Genome ORF Reader) is a perl application to predict protein sequences encoded in viral genomes. VIGOR determines the protein coding sequences by sequence similarity searching against curated viral protein databases. Please see the wiki to see list of all supported viruses. This work has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under... -
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MORPHEUS for Fiji
A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2
... of nucleus features and a double-scale analysis of orientation can be performed. The whole algorithm is implemented as a one-click procedure, thus minimizing the user intervention and the ensuing biases and errors of human origin. By this way, MORPHEUS is intended to be a useful tool to face the issue of reproducibility in bioimage analysis. -
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MGF2MGF CH
Convert mgf mass values to their nearest elemental formula
MGF2MGF CH processes mgf files (mascot generic format). It: converts masses to their nearest elemental formula mass (provided that you supply an empirical formula), can normalise intensities to the base peak of a block of ions, produces a new file with the prefix of your choice. You: specify the input line that contains the empirical formula of the parent ion, specify the key that identifies a formula and then the formula) separated by one space character, either... -
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proTRAC
Use proTRAC to annotate genomic piRNA clusters
proTRAC detects genomic piRNA clusters. It considers all the relevant features of mapped sequence reads like the amount of 1U/10A, size and strand bias to ensure a high specificity. -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
YeastpRofile is a portable Windows form application, written in C#, to compute the profile of a genomic variable around transcription start (TSS) and termination (TTS) sites of yeast mRNAs. The profile is obtained by calculating the genome-wide Pearson correlation coefficient (R) between the genomic variable values and the TSS (or TTS) counts at incremental shifting of transcribed strand. The data of TSS and TTS counts used to compute the profiles were taken from the work of Pelechano et al. (1... -
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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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).