Search Results for "dna sequence analysis"
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Showing 15 open source projects for "dna sequence analysis"
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No-code email and landing page creationBuilt for speed and collaboration, Knak streamlines campaign production with modular templates, real-time editing, simple collaboration, and seamless integrations with leading MAPs like Adobe Marketo Engage, Salesforce Marketing Cloud, Oracle Eloqua, and more. Whether you're supporting global teams or launching fast-turn campaigns, Knak helps you go from brief to build in minutes—not weeks. Say goodbye to bottlenecks and hello to marketing agility.
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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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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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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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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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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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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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NLP-Models-Tensorflow
Gathers machine learning and Tensorflow deep learning models for NLP
NLP-Models-Tensorflow is a collection of natural language processing model implementations built using the TensorFlow deep learning framework. The repository provides numerous examples of neural network architectures used in modern NLP research and applications, including text classification, language modeling, machine translation, and sentiment analysis. Each model implementation is designed to illustrate how common NLP architectures operate, such as recurrent neural networks, convolutional... -
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jieba
Stuttering Chinese word segmentation
"Jaba" Chinese word segmentation, do the best Python Chinese word segmentation component. Four word segmentation modes are supported. Precise mode, which tries to cut the sentence most precisely, suitable for text analysis. Full mode, scans all the words that can be formed into words in the sentence, the speed is very fast, but the ambiguity cannot be resolved. The search engine mode, on the basis of the precise mode, divides the long words again to improve the recall rate, which is suitable for word segmentation in search engines. The paddle mode uses the PaddlePaddle deep learning framework to train the sequence labeling (bidirectional GRU) network model to achieve word segmentation. ... -
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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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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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Awesome Recurrent Neural Networks
A curated list of resources dedicated to RNN
A curated list of resources dedicated to recurrent neural networks (closely related to deep learning). Provides a wide range of works and resources such as a Recurrent Neural Network Tutorial, a Sequence-to-Sequence Model Tutorial, Tutorials by nlintz, Notebook examples by aymericdamien, Scikit Flow (skflow) - Simplified Scikit-learn like Interface for TensorFlow, Keras (Tensorflow / Theano)-based modular deep learning library similar to Torch, char-rnn-tensorflow by sherjilozair, char-rnn... -
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DocCO
Non-disjoint groupping of Documents based on word sequence approach
This is a GUI for learning non disjoint groups of documents based on Weka machine learning framework. It offers the possibility to make non disjoint clustering of documents using both vectorial and sequential representation (word sequence approach based on WSK kernel). All data format supported by WEKA could be used in DocCO. Data could be loaded from files, from databases or from specified URL. All the preprocessing techniques implemented in WEKA could be used before performing the learning. -
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A java tool for anytime and interactive sequence mining. Aims at providing users with a way of analyzing her activity traces and extract activity schemes from them.
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FlexCRFs: A Flexible Conditional Random Fields Toolkit for Labeling and Segmenting Sequence Data (this includes a parallel implementation of CRFs called PCRFs to support training CRF models on massively parallel computer systems).
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Nemotron 3 Nano
LL model providing reasoning and conversational capabilities
...The model contains roughly 30 billion parameters and is designed to balance performance and computational efficiency, making it suitable for developers building AI applications that cannot run extremely large models. It is trained from scratch and built using a hybrid architecture that integrates Transformer attention layers with Mamba-style sequence modeling components inside a Mixture-of-Experts framework. This architecture allows the system to maintain strong reasoning capabilities while improving throughput and reducing the computational cost associated with large context processing. The model is designed as a general-purpose language system capable of handling tasks such as chat interaction, coding assistance, document analysis, and instruction following.
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