Search Results for "dna sequence analysis" - Page 4
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Showing 396 open source projects for "dna sequence analysis"
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IT Asset Management (ITAM) SoftwareEZO AssetSonar is a comprehensive IT asset management platform that provides real-time visibility into your entire digital infrastructure. Track and optimize hardware, software, and license management to reduce risks, control IT spend, and improve compliance.
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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KMWin
Kaplan-Meier for Windows
KMWin (Kaplan-Meier for Windows) is a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis. The programme is based on the statistical software environment R and provides an easy to use graphical interface. As an introduction, see http://dx.plos.org/10.1371/journal.pone.0038960#s2. -
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EMA Toolbox
Eye Movement Analysis Toolbox
...Sabatini. The Saccade Main Sequence Revised: a Fast and Repeatable Tool for Oculomotor Analysis, Behavior Research Methods, http://link.springer.com/article/10.3758/s13428-020-01388-2. -
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altanalyze
Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as... -
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. ... -
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FOSS license
FOSS license and sentence token
We propose a method to mark the comments of license as sentence-token. We use the term sentence-token to refer to a sentence of a known license. A license (both by-inclusion or by-reference) is a sequence of sentence-tokens. Sentence-tokens are generalized using one or more regular expressions. we propose an idea for license identification based on the analysis of each sentence in the license statement of a source code file. -
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MIRA V5 is available only on GitHub! The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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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. ... -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. 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... -
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OpenSeq2Seq
Toolkit for efficient experimentation with Speech Recognition
OpenSeq2Seq is a TensorFlow-based toolkit for efficient experimentation with sequence-to-sequence models across speech and NLP tasks. Its core goal is to give researchers a flexible, modular framework for building and training encoder–decoder architectures while fully leveraging distributed and mixed-precision training. The toolkit includes ready-made models for neural machine translation, automatic speech recognition, speech synthesis, language modeling, and additional NLP tasks such as sentiment analysis. ... -
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Prepack
A JavaScript bundle optimizer
A tool for making JavaScript code run faster. Prepack is still in an early development stage and not ready for production use just yet. Please try it out, give feedback, and help fix bugs. Prepack is a tool that optimizes JavaScript source code: Computations that can be done at compile-time instead of run-time get eliminated. Prepack replaces the global code of a JavaScript bundle with equivalent code that is a simple sequence of assignments. This gets rid of most intermediate computations... -
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PhageTerm
Determining Bacteriophage Termini and Packaging using NGS data.
NEW VERSION (PhageTermVirome) AVAILABLE AT : (To access the lightest version) https://gitlab.pasteur.fr/vlegrand/ptv/-/releases This new version is now compatible with PYTHON3 and now allows the analysis of multiple phage genomes/contigs (multifasta) in a single analysis. However, like before, you can still perform the analysis on a single phage genome/contig. Description : PhageTerm and PhageTermVirome are a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. ... -
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inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for...
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ART-DeCo
ART-DeCo uses polymorphism allelic ratio to predict contaminations
ART-DeCo (Allelic Ratio based Tool for Detection of Contamination) has been designed to detect contamination in constitutional NGS analysis. The tool uses the allelic ratio (AR) of Single Nucleotide Polymorphisms (SNPs) sequenced within regions of interest. When a sample is contaminated by DNA with a different genotype, unexpected ARs are obtained. Those are in turn used for detection of contamination with a screening test, followed by identification and quantification of the contaminant. ... -
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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. -
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dmrs
Comprehensive evaluation of differential methylation analysis methods
With advances in next generation sequencing technologies, bisulfite conversion of genomic DNA followed by sequencing has become the predominant technique for quantifying DNA methylation genome-wide at single base resolution. A large number of computational approaches are available in the literature for identifying differentially methylated regions in bisulfite sequencing data, with more being developed continuously. Here, we focus on a comprehensive evaluation of commonly used differential methylation analysis methods to lay out potential strengths and limitations of each method. ... -
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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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spark-msna
Algorithm on Spark for aligning multiple similar DNA/RNA sequences
The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, an unsupervised learning based on clustering technique is used to create a knowledge base to guide them. -
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Pipebar
A fast and accurate pipeline for DNA barcoding analysis.
Molecular analyses require the use of multiple bioinformatics tools. Here we proposed a pipeline for DNA chromatograms analysis of Sanger platform by open-source tools integration in order to reduce cost with standard commercial licences ensuring high quality, robustness with reduced time. Pipebar is a python application created to automatization of processing chromatogram trace files to high-quality DNA sequences for downstream analyses. -
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BioSeq
A simple GUI for some of the biological sequence analysis.
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The Deep Review
A collaboratively written review paper on deep learning, genomics, etc
This repository is home to the Deep Review, a review article on deep learning in precision medicine. The Deep Review is collaboratively written on GitHub using a tool called Manubot (see below). The project operates on an open contribution model, welcoming contributions from anyone. To see what's incoming, check the open pull requests. For project discussion and planning see the Issues. As of writing, we are aiming to publish an update of the deep review. We will continue to make project... -
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SGA Conversion and Analysis Tool
Convert SGA format multimedia files to PNG and AVI format
This program is a utility for viewing, analyzing, and converting the data in SGA format multimedia files used by Digital Pictures in their games for the Sega Mega CD, Sega Super 32X, Sega Saturn, 3DO video game systems, and Windows PCs into formats that can be read by media player software on modern PCs. -
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The automatic quantification of foci on fluorescent images of cells after DNA damage is widely used for estimation of the DNA double-strand break number in DNA of single cells. We present a graphical user interface FoCo, which was developed in Matlab together with ImageJ for individual foci count using image analysis.
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idwtree
Assigns orthologs using a phylogenetic tree
Protein BLAST analysis finds all homologs of a protein; however, for many analyses, it is important to identify orthologs in different species (e.g. homologs that derive from the same ancestral sequence). The program idwtree aid in this analysis by assigning 'group' identity in phylogenetic trees containing reference sequences as markers. The standard workflow idwtree was intended to analyze: 1. -
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CRISPRamplicon
A tool for analysis of Genome editing outcomes from sequencing data
CRISPR-Cas9 is a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence. It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications. Here, a cost-effective and high-throughput strategy was developed for identifying CRISPR/Cas-induced mutations via CRISPR Amplicon Sequencing (Xie’s lab, http://www.biootools.com/). In particular, we have developed a new bioinformatics tool named CRISPRamplicon, which can be used for analysis of CRISPR/Cas9 genome editing outcomes for high-throughput sequencing data with fast speed.
