Search Results for "dna sequence analysis"
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Showing 397 open source projects for "dna sequence analysis"
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Discourse Network Analyzer (DNA)
Discourse Network Analyzer (DNA)
The Java software Discourse Network Analyzer (DNA) is a qualitative content analysis tool with network export facilities. You import text files and annotate statements that persons or organizations make, and the program will return network matrices of actors connected by shared concepts. -
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
ProSeq ('Processor of sequences') is a package including GUI and command line programs to process and analyse DNA polymorphism data. It allows one to open and save sequence data in over a dozen file formats (and convert between these formats). It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. ProSeq4 includes tools to analyse DNA polymorphism, scan for selection, do PCA and reconstruct phylogenies from sequence or SNP data. ... -
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doccano
Open source annotation tool for machine learning practitioners
doccano is an open-source text annotation tool for humans. It provides annotation features for text classification, sequence labeling and sequence-to-sequence tasks. So, you can create labeled data for sentiment analysis, named entity recognition, text summarization and so on. Just create a project, upload data and start annotating. You can build a dataset in hours. -
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binocular
Binocular segmentation of whole-genome DNA sequence data
Segmentation-based detection of copy-number alterations and allelic imbalances in whole-genome DNA sequence data. -
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Evo 2
Genome modeling and design across all domains of life
Evo 2 is a DNA language model system designed for long-context genome modeling and biological sequence design across all domains of life. The project models DNA at single-nucleotide resolution and supports context windows of up to one million base pairs, which places it in a class of models built for very large genomic reasoning tasks. According to the repository, it uses the StripedHyena 2 architecture, was pretrained with Savanna, and was trained autoregressively on the OpenGenome2 dataset containing 8.8 trillion tokens. ... -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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Plaso
Super timeline all the things
Plaso (Plaso Langar Að Safna Öllu), or "super timeline all the things," is a Python-based engine designed for automatic creation of timelines in digital forensic investigations. It processes various log files and artifacts to generate a chronological sequence of events, aiding analysts in understanding system activities. -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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ReachabilityAnalysis.jl
Compute reachable states of dynamical systems
Reachability analysis is concerned with computing rigorous approximations of the set of states reachable by a dynamical system. In the scope of this package are systems modeled by continuous or hybrid dynamical systems, where the dynamics change with discrete events. Systems are modeled by ordinary differential equations (ODEs) or semi-discrete partial differential equations (PDEs), with uncertain initial states, uncertain parameters or non-deterministic inputs. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
...Additionally, loading sequences from FASTA or text files is supported, making it convenient for users to work with existing sequence data. Enjoy exploring the functionalities provided by this GUI app for basic sequence analysis! -
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Profile Data
Analyze computation-communication overlap in V3/R1
profile-data is a repository that publishes profiling traces and metrics from DeepSeek’s training and inference infrastructure (especially during DeepSeek-V3 / R1 experiments). The profiling data targets insights into computation-communication overlap, pipeline scheduling (e.g. DualPipe), and how MoE / EP / parallelism strategies interact in real systems. The repository contains JSON trace files like train.json, prefill.json, decode.json, and associated assets. Users can load them into tools... -
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AQUAD
Software for Analysis of Qualitative Data
AQUAD Eight is available in English, German, and Spanish with separate modules for the analysis of texts, audios, videos, graphic files, and a complementary module for exploratory statistical analysis with R. The modules follow the coding paradigm of qualitative analysis, offering for text analysis also functions for sequence analysis (Objective Hermeneutics) and word based quantitative analysis. -
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This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs. Online webserver https://shinywgcna.serve.scilifelab.se/app/shinywgcna PLEASE NOTE Datasets with larger dimensions (e.g., 1000x100) may fail on the server,because it is only running on 1GB RAM allocation. ...
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom parameter combinations if in-depth analysis is necessary or advised in e.g. low read rate situations. ... -
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Python Zero to Hero for DevOps Engineers
Learn Python from DevOps Engineer point of you
Python Zero to Hero for DevOps Engineers is a structured “Python Zero to Hero for DevOps Engineers” course laid out as a day-by-day learning path. The repository is organized into Day-01 through Day-19 folders plus a small sample app, which makes it very easy to follow in sequence like a bootcamp. The curriculum starts with Python installation, environment setup, and writing your first script, then quickly moves into data types, strings, regular expressions, variables, and functions. It places a strong emphasis on DevOps-specific use cases: environment variables, command-line arguments, configuration handling, and automating log analysis or user management tasks are all explicitly woven into the exercises. ... -
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popoolation
estimate natural variation and positive selection
...One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https://sourceforge.net/p/popoolation/wiki/Main/ -
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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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ArchCUT3-D
ArchCUT3-D: 3-D Analysis of Incised Archeological Surfaces
Software developed to precisely evaluate the 3-D micromorphological characteristics of archaeological surface incisions. Analysis based on a continuous 3-D slice sequence from a chosen range within the incision path. Measurements and shapes of individual slices can be extracted. ArchCUT3-D’s interface is designed to provide a computational and mathematical analysis of engravings to a wide audience. Please cite Dubinsky, L., David, M., & Grosman, L. (2023). ... -
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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CometAnalyser
CometAnalyser, for quantitative comet assay analysis.
Description: Comet assay provides an easy solution to estimate DNA damage in single cells through microscopy assessment. To obtain reproducible and reliable quantitative data, we developed an easy-to-use tool named CometAnalyser. CometAnalyser is an open-source deep-learning tool designed for the analysis of both fluorescent and silver-stained wide-field microscopy images. Once the comets are segmented and classified, several intensity/morphological features are automatically exported as a spreadsheet file. ... -
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MetaEntropy
R package for Virome Mutational Analysis
Estimates Shannon entropy, per gene and per genomic position, associated with non-synonymous mutation frequencies in viral populations, such as wastewater samples. The package uses codon translations for functional insights. Each amino acid can be treated as an individual state, resulting in a 20-state entropy computation, or grouped into one of six physicochemical classes, adding further functional context. Provides normalized values (0-1 scale) to facilitate the direct comparison of... -
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RABV-GUI
Interface for rabies virus sequence analysis and Genbank submission
RABV-GUI is a graphical user interface designed for running RABV-GLUE, specifically to facilitate GenBank submissions for rabies sequences. In addition to supporting GenBank submissions, RABV-GUI has been updated with the latest rabies sequences and can perform database queries similar to those available on the RABV-GLUE website (http://rabv-glue.cvr.gla.ac.uk/).
