Projects in Awesome Lists by MaayanLab
A curated list of projects in awesome lists by MaayanLab .
https://github.com/maayanlab/clustergrammer
An interactive heatmap visualization built using D3.js
biology clustering d3 heatmap jupyter-notebook jupyter-widget python visualization
Last synced: 05 Apr 2025
https://github.com/MaayanLab/clustergrammer
An interactive heatmap visualization built using D3.js
biology clustering d3 heatmap jupyter-notebook jupyter-widget python visualization
Last synced: 21 Dec 2024
https://github.com/maayanlab/biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
bioinformatics cloud dcppc jupyter notebook pipeline rna-seq systems-biology
Last synced: 05 Apr 2025
https://github.com/maayanlab/zika-rnaseq-pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
bioinformatics-pipeline jupyter-notebook notebook pipeline rna-seq rna-seq-analysis
Last synced: 21 Nov 2024
https://github.com/maayanlab/archs4
ARCHS4 RNA-seq processing scripts and web server pages.
Last synced: 21 Nov 2024
https://github.com/maayanlab/clustergrammer-widget
The Clustergrammer interactive Jupyter notebook widget
clustering jupyter-notebook jupyter-widget pandas-dataframe python visualization
Last synced: 21 Nov 2024
https://github.com/maayanlab/appyter-catalog
A catalog of appyter notebooks
Last synced: 06 Apr 2025
https://github.com/maayanlab/blitzgsea
Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.
Last synced: 21 Nov 2024
https://github.com/maayanlab/biojupies-plugins
User-submitted RNA-seq data analysis tools for BioJupies.
bioinformatics jupyter systems-biology
Last synced: 21 Nov 2024
https://github.com/maayanlab/archs4py
Python package to load and query ARCHS4 data
Last synced: 21 Nov 2024
https://github.com/maayanlab/maayanlab-bioinformatics
A collection of useful functions for bioinformatics data analysis
Last synced: 21 Nov 2024
https://github.com/maayanlab/clustergrammer-py
A python module for the clustergrammer matrix visualization project that creates the JSON object for the front-end JavaScript portion of Clustergrammer.
Last synced: 21 Nov 2024
https://github.com/maayanlab/geo2enrichr
A browser extension and web application for extracting gene sets from GEO and piping them to Enrichr.
Last synced: 21 Nov 2024
https://github.com/maayanlab/playbook-workflow-builder
A repository for the Playbook Workflow Builder project.
bioinformatics biology cwl data-science gene-expression gene-ontology gene-sets proteomics rna-seq-analysis systems-biology workflow
Last synced: 21 Nov 2024
https://github.com/maayanlab/clustergrammer-docs
The documentation for the Clustergrammer project
Last synced: 21 Nov 2024
https://github.com/maayanlab/sep-l1000
Website for visualizing predicted drug side-effects using L1000 data (http://maayanlab.net/SEP-L1000/)
Last synced: 21 Nov 2024
https://github.com/maayanlab/clustergrammer-web
Create a clustergram visualization from a user defined network in tsv format.
Last synced: 21 Nov 2024
https://github.com/maayanlab/react-scatter-board
A reusable React library for interactive THREE.js 2d/3d scatter plots
Last synced: 21 Nov 2024
https://github.com/maayanlab/ccle_clustergrammer
Visualize CCLE gene expression data using Clustergrammer.
Last synced: 21 Nov 2024
https://github.com/maayanlab/geode
A Python implementation of the R package GeoDE
Last synced: 21 Nov 2024
https://maayanlab.github.io/CCLE_Clustergrammer/
Visualize CCLE gene expression data using Clustergrammer.
Last synced: 14 Nov 2024
https://github.com/maayanlab/slackbot-tutorial
A simple tutorial on how to build a slack app (with python and flask)
slack slack-api slack-app slack-bot slack-commands
Last synced: 14 Apr 2025
https://github.com/maayanlab/intro-rnaseq-jupyter
Building RNA-seq Analysis Pipelines with Jupyter
Last synced: 21 Nov 2024
https://github.com/maayanlab/signature-commons-ui
A front-end UI for demoing API integration
Last synced: 21 Nov 2024
https://github.com/maayanlab/rna-seq-benchmarking
R codes for the benchmarking of 2 aligners (STAR and Kallisto) and 6 differential expression analysis methods (DESeq2, edgeR, limma-voom, CD, t-test, fold change) in RNA-Seq
Last synced: 21 Nov 2024
https://github.com/maayanlab/covid19_crowd_library
COVID-19 Crowd Generated Gene and Drug Set Library
covid-19 covid19-data drug-sets gene-sets
Last synced: 21 Nov 2024
https://github.com/maayanlab/scavi
Single-cell RNA-seq data analysis and visualization
Last synced: 21 Nov 2024
https://github.com/maayanlab/genesetr
Manipulate, Test, and Visualize Gene Set Overlaps
Last synced: 21 Nov 2024
https://github.com/maayanlab/paea
Shiny app for Characteristic Direction and Principal Angle Enrichment Analysis (PAEA)
Last synced: 21 Nov 2024
https://github.com/maayanlab/join-collections
This repository contains Jupyter Notebooks selected a Collection in the Journal of Interactive Notebooks (JOIN). More info can be found at https://amp.pharm.mssm.edu/join/
Last synced: 15 Mar 2025
https://github.com/maayanlab/smartapis
Smart API specifications for various Ma'ayan Lab Tools
Last synced: 21 Nov 2024
https://github.com/maayanlab/genes2networks
Tool for Creating Subnetworks from Lists of Mammalian Genes or Proteins
Last synced: 15 Mar 2025
https://github.com/maayanlab/enrichment_sandbox
Benchmarking enrichment analysis algorithms using transcription factor-gene and drug-gene libraries.
Last synced: 15 Mar 2025
https://github.com/maayanlab/archs4-api
An API for serving ARCHS4 Data from H5 over S3
Last synced: 15 Mar 2025
https://github.com/maayanlab/server-templates
Docker containers of preconfigured servers and web application stacks.
Last synced: 21 Nov 2024
https://github.com/maayanlab/datasets2tools
Source code repository for the Datasets2Tools project.
analyses bioinformatics datasets index tools
Last synced: 21 Nov 2024
https://github.com/maayanlab/l1000fwd
Large-scale visualization of drug-induced transcriptomic signatures
data-visualization drug-discovery threejs
Last synced: 21 Nov 2024
https://github.com/maayanlab/harmonizome_processing_scripts
Scripts for processing datasets for the Harmonizome
Last synced: 15 Mar 2025
https://github.com/maayanlab/enrichrpythonscripts
Python Jupyter notebooks for Enrichr species databases
Last synced: 21 Nov 2024
https://github.com/maayanlab/lists2networks
Integrated Analysis of Gene/Protein Lists
Last synced: 15 Mar 2025
https://github.com/maayanlab/gtextissuenotebooks
Visualization and analysis of RNA-seq data from GTEx v8 in Jupyter Notebooks
Last synced: 15 Mar 2025
https://github.com/maayanlab/drugmonizome-ml
Drugmonizome-ML – predict drugs for COVID-19 with drugmonizome and machine learning
Last synced: 21 Nov 2024
https://github.com/maayanlab/memaboard
Multidimensional visualization of MEP-LINCS datasets using the tensorboard platform.
Last synced: 15 Mar 2025
https://github.com/maayanlab/iris_clustergrammer_visualization
Visualizing the Iris machine learning visualization using Clustergrammer
Last synced: 15 Mar 2025
https://github.com/maayanlab/dokku
Ma'ayanlab dokku server admin and user guide
Last synced: 31 Mar 2025
https://github.com/maayanlab/kea2
Kinase enrichment analysis at the phosphosite and protein levels
Last synced: 15 Mar 2025
https://github.com/maayanlab/creeds
The web application for the crowdsourced gene expression signatures: http://amp.pharm.mssm.edu/creeds/
Last synced: 21 Nov 2024
https://github.com/maayanlab/cst_lung_cancer_viz
CST Lung Cancer PTM visualizations
Last synced: 21 Nov 2024
https://github.com/maayanlab/graph-dr
Benchmarks of dimensionality reduction algorithms
autoencoder cytoscape dimensionality-reduction force-layout graph-algorithms graph-theory manifold-learning
Last synced: 21 Nov 2024
https://github.com/maayanlab/bioinput
A JavaScript library to quickly and easily implement an autocomplete html input element for various biological entities.
Last synced: 15 Mar 2025
https://github.com/maayanlab/druglib_enrichment_comparison
Comparison of drug target libraries using enrichment analysis.
Last synced: 15 Mar 2025
https://github.com/maayanlab/react-supervenn
An interactive React implementation of supervenn
Last synced: 15 Mar 2025
https://github.com/maayanlab/mepmosaic
Sourcecode for http://amp.pharm.mssm.edu/MEPmosaic
Last synced: 15 Mar 2025
https://github.com/maayanlab/human-melanoma-signature
Analysis of melanoma signatures from RNA seq data
Last synced: 15 Mar 2025
https://github.com/maayanlab/hyposet
An interactive web application for set overlap inspection.
Last synced: 15 Mar 2025
https://github.com/maayanlab/kinase_substrate_similarity_network
An example visualization of a kinase-substrate similarity network using Clustergrammer.
Last synced: 15 Mar 2025
https://github.com/maayanlab/signature-commons
A docker-compose for deploying the entire signature-commons stack
Last synced: 15 Mar 2025
https://github.com/maayanlab/adhesome-prediction
Predicting whether a gene is adhesome components based on OMIC features
Last synced: 15 Mar 2025
https://github.com/maayanlab/dmoa-embed
Embedding visualizer for the DMOA signatures.
Last synced: 15 Mar 2025
https://github.com/maayanlab/enrichr_api
REST APIs provided by Enrichr
api enrichment-analysis enrichr
Last synced: 15 Mar 2025
https://github.com/maayanlab/harmonizome-data-processing-appyters
Converting Harmonizome Python scripts into Appyters
Last synced: 15 Mar 2025
https://github.com/maayanlab/kubernetes-auto-ingress
Auto-generate kubernetes ingresses based on a deployment annotation.
Last synced: 15 Mar 2025
https://github.com/maayanlab/datasets2tools-datamed
Implementation of the Datasets2Tools interface for the DataMed portal.
Last synced: 15 Mar 2025
https://github.com/maayanlab/gelb_zf
Scripts and Notebooks used for analyzing the Zebrafish RNA-Seq data from Dr. Gelb
Last synced: 15 Mar 2025
https://github.com/maayanlab/ljp
LINCS Joint Project (LJP) Breast Cancer Network Browser: http://amp.pharm.mssm.edu/LJP/
Last synced: 15 Mar 2025
https://github.com/maayanlab/drugbot
Contains code and website for the DrugBot Slack Application
Last synced: 15 Mar 2025