Sequences

A collection of 90 posts

MetalSite: alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

MetalSite: alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

MetalSite: alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

04 September 2022

The Monod package fits CME models to sequencing data

The Monod package fits CME models to sequencing data

25 July 2022

Generate (message) sequence diagrams from TLA+ state traces

Generate (message) sequence diagrams from TLA+ state traces

05 March 2022

Library to play with filtering numeric sequences by sums of their pairs, triplets, etc. With a bonus CLI demo

Library to play with filtering numeric sequences by sums of their pairs, triplets, etc. With a bonus CLI demo

18 February 2022

En- and decrypting text-messages by creating a key with of the fibonacci-sequence

En- and decrypting text-messages by creating a key with of the fibonacci-sequence

17 February 2022

Temporal Alignment Prediction for Supervised Representation Learning and Few-Shot Sequence Classification

Temporal Alignment Prediction for Supervised Representation Learning and Few-Shot Sequence Classification

16 February 2022

Generating the Fibonacci sequence is a classic recursive problem

Generating the Fibonacci sequence is a classic recursive problem

15 February 2022

Minimal implementaion of Decision Transformer: Reinforcement Learning via Sequence Modeling in PyTorch for mujoco control tasks in OpenAI gym

Minimal implementaion of Decision Transformer: Reinforcement Learning via Sequence Modeling in PyTorch for mujoco control tasks in OpenAI gym

Minimal implementaion of Decision Transformer: Reinforcement Learning via Sequence Modeling in PyTorch for mujoco control tasks in OpenAI gym

14 February 2022

Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2

Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2

10 February 2022

Doughskript interpreter for converting simple command sequences into executable Arduino C++ code

Doughskript interpreter for converting simple command sequences into executable Arduino C++ code

10 February 2022

Iterative refinement graph neural network for antibody sequence-structure co-design (RefineGNN)

Iterative refinement graph neural network for antibody sequence-structure co-design (RefineGNN)

03 February 2022

Simple software to calculate susequence with highest sum

Simple software to calculate susequence with highest sum

01 February 2022

Sequential prediction learning framework and algorithm

Sequential prediction learning framework and algorithm

Sequential prediction learning framework and algorithm

25 January 2022

Linux GUI app to codon optimize many single-fasta files with coding sequences , using many taxonomy ids

Linux GUI app to codon optimize many single-fasta files with coding sequences , using many taxonomy ids

Linux GUI app to codon optimize many single-fasta files with coding sequences , using many taxonomy ids

23 January 2022

Train large COMET (T5-3B/GPT2-XL) with small memory (on 11GB memory GPUs like 1080/2080) using DeepSpeed

Train large COMET (T5-3B/GPT2-XL) with small memory (on 11GB memory GPUs like 1080/2080) using DeepSpeed

23 January 2022

Sequitur : A Library of autoencoders for sequential data

Sequitur : A Library of autoencoders for sequential data

Sequitur : A Library of autoencoders for sequential data

23 January 2022

Machine Learning

A machine learning project that predicted binding sites of AP1 transcription factor, using ChIP-Seq data and local DNA shape information

AP1 Transcription Factor Binding Site Prediction

22 January 2022

A pipeline to analyse transposon directed insertion-site sequencing

A set of tools to analyse the output from TraDIS analyses

22 January 2022

Pipeline code for Sequential-GAM(Genome Architecture Mapping)

Pipeline code for Sequential-GAM(Genome Architecture Mapping)

19 January 2022

ParaGen - A PyTorch deep learning framework for parallel sequence generation

ParaGen - A PyTorch deep learning framework for parallel sequence generation

19 January 2022

Use the Seq2Seq method to implement machine translation and introduce Attention mechanism to improve the results

Use the Seq2Seq method to implement machine translation and introduce Attention mechanism to improve the results

19 January 2022

Deep learning transformer model that generates unique music sequences

Deep learning transformer model that generates unique music sequences

18 January 2022

SCROLLS: Standardized CompaRison Over Long Language Sequences

SCROLLS: Standardized CompaRison Over Long Language Sequences

12 January 2022

Example of a Viterbi algorithm applied to a hidden Markov model on DNA sequence

Example of a Viterbi algorithm applied to a hidden Markov model on DNA sequence

11 January 2022

Creates a magic square by randomly generating a list until the list happens to be a magic square

Creates a magic square by randomly generating a list until the list happens to be a magic square

01 January 2022

An easy to use GUI based video to image sequence converter (and vice versa)

An easy to use GUI based video to image sequence converter (and vice versa)

An easy to use GUI based video to image sequence converter (and vice versa)

27 December 2021

Sequence lineage information extracted from RKI sequence data repo

Sequence lineage information extracted from RKI sequence data repo

Sequence lineage information extracted from RKI sequence data repo

26 December 2021

Extracts essential Mediapipe face landmarks and arranges them in a sequenced order

Extracts essential Mediapipe face landmarks and arranges them in a sequenced order

26 December 2021

A toolkit to generate MR sequence diagrams

A toolkit to generate MR sequence diagrams

A toolkit to generate MR sequence diagrams

24 December 2021

The scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation

The scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation

23 December 2021

Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history

Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history

23 December 2021

A modular sequencer based on Pi Pico & EuroPi

A modular sequencer based on Pi Pico & EuroPi

23 December 2021

Dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap

Dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap

19 December 2021

Annotates sequences with Eggnog-mapper and hhblits against PDB70

Annotates sequences with Eggnog-mapper and hhblits against PDB70

18 December 2021

Annotates sequences with Eggnog-mapper and hhblits against PDB70

Annotates sequences with Eggnog-mapper and hhblits against PDB70

18 December 2021

3D

A minimal, standalone viewer for 3D animations stored as stop-motion sequences of individual .obj mesh files

A minimal, standalone viewer for 3D animations stored as stop-motion sequences of individual .obj mesh files

14 December 2021

ScisorWiz: Differential Isoform Visualizer for Long-Read RNA Sequencing Data

ScisorWiz: Differential Isoform Visualizer for Long-Read RNA Sequencing Data

11 December 2021

Cash in on Expressed Barcode Tags (EBTs) from NGS Sequencing Data with Python

Cash in on Expressed Barcode Tags (EBTs) from NGS Sequencing Data with Python

08 December 2021

Simple, high-school-leveled sequence library written in Python

Simple, high-school-leveled sequence library written in Python

05 December 2021

Big Bird: Transformers for Longer Sequences

Big Bird: Transformers for Longer Sequences

04 December 2021

Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thalia

Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thalia

04 December 2021

Official codebase for Decision Transformer: Reinforcement Learning via Sequence Modeling

Official codebase for Decision Transformer: Reinforcement Learning via Sequence Modeling

Official codebase for Decision Transformer: Reinforcement Learning via Sequence Modeling

03 December 2021

PyTorch trainer and model for Sequence Classification

PyTorch trainer and model for Sequence Classification

03 December 2021

Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thaliana

Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thaliana

03 December 2021

A functional mutable sequence inheriting from Python's built-in list

A functional mutable sequence inheriting from Python's built-in list

03 December 2021

Tools to create pixel-wise object masks, bounding box labels and 3D object model for object sequences filmed

Tools to create pixel-wise object masks, bounding box labels and 3D object model for object sequences filmed

Tools to create pixel-wise object masks, bounding box labels and 3D object model for object sequences filmed

29 November 2021

Statistical tests for the sequential locality of graphs

Statistical tests for the sequential locality of graphs

25 November 2021

PRIP：A Protein-RNA Interface Predictor Based on Semantics of Sequences

PRIP：A Protein-RNA Interface Predictor Based on Semantics of Sequences

PRIP：A Protein-RNA Interface Predictor Based on Semantics of Sequences

25 November 2021