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
anomaly-detection dask data-science matrix-profile motif-discovery numba pattern-matching pydata python time-series-analysis time-series-data-mining time-series-segmentation
Language:Python 3695
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 734
matrix-profile-foundation / matrixprofile
A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms, accessible to everyone.
algorithms anomaly-detection clustering data-mining data-science hacktoberfest matrixprofile motif-discovery python python2 python3 segmentation time-series time-series-analysis
Language:Python 363
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 84
aplbrain / dotmotif
A performant, powerful query framework to search for network motifs
graph query-language motifs motif-discovery python connectomics connectome neo4j graph-database subgraph-isomorphism graph-matching networkx vf2 aplbrain bossdb dotmotif
Language:Python 81
patrickzib / motiflets
Motiflets
dataseries motif motif-discovery motifs pattern pattern-discovery pattern-recognition time-series time-series-analysis timeseries unsupervised-learning
Language:Jupyter Notebook 46
GreenleafLab / motifmatchr
Fast motif matching in R
bioinformatics r motif-discovery
Language:C++ 43
baggepinnen / MatrixProfile.jl
Time-series analysis using the Matrix profile in Julia
matrix-profile time-series time-series-analysis outlier-detection motif-discovery similarity-search signal-processing dsp anomaly-detection clustering motif-analysis data-mining change-point-detection predictive-maintenance
Language:Julia 33
asntech / pyjaspar
pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
gene-regulation jaspar motif-discovery motifs tf-binding-motif transcription-factor-binding transcription-factors
Language:Python 24
ksanjeevan / ts-motif-detection
Time Series Motif Detection in Python
motif-discovery
Language:Python 20
ML-KULeuven / locomotif
LoCoMotif is a time series motif discovery method that discovers variable-length motif sets in multivariate time series using time warping
motif-discovery multivariate pattern-mining time-series time-warping unsupervised-learning variable-length
Language:Jupyter Notebook 20
shao-lab / MotifScan
A motif discovery tool to detect the occurrences of known motifs
bioinformatics motif-discovery transcription-factors
Language:Python 20
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
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.
motif-discovery motif-analysis chip-seq bioinformatics ngs-analysis
Language:C++ 13
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 12
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 / 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++ 10
saketkc / moca
:m: Tool for motif conservation analysis
bioinformatics chip-seq motif-discovery transcription-factor-binding transcription-factors
Language:PostScript 9
BIMSBbioinfo / RCAS
R package for the RNA Centric Annotation System (RCAS)
bioconductor cage coverage-distribution go interactive-plots modification motif-discovery msigdb par-clip protein-rna-interactions reporting rna
Language:R 7
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
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
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
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 4
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.
motif-analysis motif-discovery pwm transcription-factor-binding transcription-factors
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
frankchen121212 / RHSNet
Tensorflow and Keras implementation of RHSNet for recombination hotspot identification and quantification
deep-neural-networks motif-discovery computational-biology
Language:Jupyter Notebook 3
iyak / RNAelem
RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.
bioinformatics rna-structure motif-discovery
Language:C++ 3
psaisan / CARTMAN
CARTMAN: Co-occurrence Analysis of Repeating Transcription-factor Motifs And Networks
co-occurence-network computational-biology epigenomics gene-regulation motif-discovery genomics transcription-factors
Language:Jupyter Notebook 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