motif-discovery

There are 8 repositories under motif-discovery topic.

TDAmeritrade / stumpy
STUMPY is a powerful and scalable Python library for modern time series analysis
data-science time-series-analysis dask numba python anomaly-detection pattern-matching pydata matrix-profile motif-discovery time-series-segmentation time-series-data-mining
Language:Python 2984
target / matrixprofile-ts
A Python library for detecting patterns and anomalies in massive datasets using the Matrix Profile
python time-series data-science matrix-profile python3 motif-discovery motif pip pip3 pypi-packages pypi timeseries-analysis timeseries-segmentation
Language:Python 729
matrix-profile-foundation / matrixprofile
A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms, accessible to everyone.
python time-series algorithms data-science data-mining python3 python2 matrixprofile time-series-analysis motif-discovery anomaly-detection segmentation clustering hacktoberfest
Language:Python 354
matrix-profile-foundation / go-matrixprofile
golang library for computing matrix profiles along with other time series analysis features
matrix-profile golang anomaly-detection motif-discovery timeseries-analysis timeseries-segmentation
Language:Go 82
aplbrain / dotmotif
A performant, powerful query framework to search for network motifs
aplbrain bossdb connectome connectomics dotmotif graph graph-database graph-matching motif-discovery motifs neo4j networkx python query-language subgraph-isomorphism vf2
Language:Python 80
patrickzib / motiflets
Motiflets
dataseries motif motif-discovery motifs pattern-recognition time-series time-series-analysis timeseries unsupervised-learning
Language:Jupyter Notebook 42
GreenleafLab / motifmatchr
Fast motif matching in R
bioinformatics r motif-discovery
Language:C++ 37
baggepinnen / MatrixProfile.jl
Time-series analysis using the Matrix profile in Julia
anomaly-detection change-point-detection clustering data-mining dsp matrix-profile motif-analysis motif-discovery outlier-detection predictive-maintenance signal-processing similarity-search time-series time-series-analysis
Language:Julia 29
ksanjeevan / ts-motif-detection
Time Series Motif Detection in Python
motif-discovery
Language:Python 20
shao-lab / MotifScan
A motif discovery tool to detect the occurrences of known motifs
bioinformatics transcription-factors motif-discovery
Language:Python 18
asntech / pyjaspar
pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
jaspar gene-regulation transcription-factor-binding transcription-factors motifs motif-discovery tf-binding-motif
Language:Python 16
macks22 / motif-classify
Classify time series data using motifs discovered from Sequitur processing of SAX discretized data.
motif-discovery time-series sequitur scikit-learn classification
Language:Python 13
Kyubyong / neurobind
Yet Another Model Using Neural Networks for Predicting Binding Preferences of for Test DNA Sequences
bioinformatics binding motif-discovery
Language:Python 11
soedinglab / BaMMmotif2
Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.
bioinformatics chip-seq motif-analysis motif-discovery ngs-analysis
Language:C++ 10
microsoft / BindVAE
Variational Auto Encoders for learning binding signatures of transcription factors
atac-seq dna-sequence motif-discovery transcription-factor vae variational-auto-encoder deep-learning dna machine-learning tensorflow
Language:Python 9
saketkc / moca
:m: Tool for motif conservation analysis
motif-discovery bioinformatics transcription-factor-binding transcription-factors chip-seq
Language:PostScript 9
mettekou / MatrixProfile
The matrix profile data structure and associated algorithms for mining time series data
fsharp dotnet data-science data-mining time-series algorithms clustering segmentation motif-discovery time-series-analysis anomaly-detection matrixprofile
Language:F# 7
soedinglab / PEnG-motif
PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
bioinformatics motif-discovery chip-seq dna rna
Language:C++ 7
mbelmadani / motifgp
Motif discovery for DNA sequences using multiobjective optimization and genetic programming.
motif genetic-programming multiobjective-optimization bioinformatics chip-seq regular-expressions network-expressions strongly-typed motif-discovery transcription-factors transcription-factor-binding python pareto-front nsga-ii deap dna sequences dna-sequences jaspar
Language:Python 6
MyersGroup / MotifFinder
An R package for de novo discovery of enriched DNA motifs (e.g. TFBS)
finding-enriched-motifs r-package tfbs tfbs-discovery motif-discovery transcription-factor-binding chip-seq
Language:R 6
pbloem / motive
A proof-of-concept library for motif analysis using MDL techniques.
motif-analysis motive proof nauty motif-discovery motif-counts motifs network-motifs network-analysis graph-analytics
Language:Java 6
temporal-graphs / STM
Structural Temporal Modeling to characterize temporal networks
temporal-networks graph motif-discovery apache-spark
Language:Jupyter Notebook 6
BIMSBbioinfo / RCAS
R package for the RNA Centric Annotation System (RCAS)
bioconductor interactive-plots par-clip cage rna modification reporting msigdb go protein-rna-interactions motif-discovery coverage-distribution
Language:R 5
icaoberg / docker-meme-suite
:whale: :computer: Docker recipe for meme-suite
genomics motif-discovery docker dockerfile docker-image meme-suite
Language:Dockerfile 5
stackedq / Motif-discovery
Motif discovery done by AI algorithms and python.
motif-discovery
Language:Python 5
Milad137 / Motif-Discovery
modified exact discovery of time series motifs
motif-discovery motifs motif
Language:Jupyter Notebook 4
soedinglab / BaMM_webserver
Webserver for motif discovery with higher-order Bayesian Markov Models (BaMMs)
bioinformatics webserver motif-discovery bamms
Language:HTML 4
tksaha / motif-finding
Finding Network Motifs Using MCMC Sampling
motif-finding motif-discovery mcmc-sampler-graph mcmc-sampler-undirected-graph
Language:C++ 4
VorontsovIE / diHOCOMOCO
Scripts for motif assessment for HOCOMOCO v10/v11.
pwm motif-discovery motif-analysis transcription-factors transcription-factor-binding
Language:Ruby 4
burkesquires / FeaVar
A python package to compute clusters of sequence feature variant types (SFVTs) based upon user-selected subsequence.
python bioinformatics sequence-alignment motif-discovery nucleotides protein-sequences clustering
Language:Clarion 3
eugene-kamenev / tsmp4j
Time Series with Matrix Profile in Java
algorithms clustering data-mining knn matrixprofile motif-analysis motif-discovery similarity-search timeseries timeseries-analysis anomaly-detection
Language:Java 3
Shuyib / Phylogenetic-tree-study
Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7
phylogenetics microorganism 16s-rrna pandas numpy-arrays bokehplots scipy hierarchical-clustering unsupervised-learning machine-learning kenya jupyter-notebook python motif-analysis motif-discovery
Language:Jupyter Notebook 3
frankchen121212 / RHSNet
Tensorflow and Keras implementation of RHSNet for recombination hotspot identification and quantification
deep-neural-networks motif-discovery computational-biology
Language:Jupyter Notebook 2
nsarang / motif_bionet
Identifying frequent patterns in graphs
motif-discovery graph-algorithms biological-networks d3-visualization graphs disjoint-motifs
Language:C++ 2
parthian-sterlet / sitega
The software package SiteGA for de novo motif search in ChIP-seq data
motif-discovery bioinformatics chip-seq long-range-dependences discriminant-analysis genetic-algorithm alternative-motif-model
Language:C++ 2
talponer / humanDPE
Identification of a functional downstream core promoter element in human promoters using an Expectation-Maximization algorithm
publication publication-code publication-data expectation-maximization-algorithm dna-motif motif-discovery
Language:R 2