Ma'ayan Lab
Developing Computational Methods to Study the Complexity of Regulatory Networks in Mammalian Cells
New York City, NY
Pinned Repositories
appyter
jinja2-enabled jupyter notebooks
appyter-catalog
A catalog of appyter notebooks
archs4
ARCHS4 RNA-seq processing scripts and web server pages.
biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
blitzgsea
Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.
clustergrammer
An interactive heatmap visualization built using D3.js
clustergrammer-widget
The Clustergrammer interactive Jupyter notebook widget
HarmonizomePythonScripts
maayanlab-bioinformatics
A collection of useful functions for bioinformatics data analysis
Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Ma'ayan Lab's Repositories
MaayanLab/biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
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.
MaayanLab/HarmonizomePythonScripts
MaayanLab/Playbook-Workflow-Builder
A repository for the Playbook Workflow Builder project.
MaayanLab/archs4py
Python package to load and query ARCHS4 data
MaayanLab/Knowledge-Graph-UI
Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries. Example implementation:
MaayanLab/rummagene
MaayanLab/prismexp
Advanced gene function prediction
MaayanLab/archs4r
R package to load and query ARCHS4 data in R
MaayanLab/EnrichrPythonScripts
Python Jupyter notebooks for Enrichr species databases
MaayanLab/rummageo
MaayanLab/server-templates
Docker containers of preconfigured servers and web application stacks.
MaayanLab/sigcom-lincs
Signature Commons LINCS Repo
MaayanLab/dokku
Ma'ayanlab dokku server admin and user guide
MaayanLab/DRC-Portals
MaayanLab/GeneSetCart
GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.
MaayanLab/archs4dx
MaayanLab/CFDECoauthorNetwork
A fork to create the CFDECoauthorNetwork.
MaayanLab/ChEA-KG
Demo of how to build a transcription factor KG using the KG UI
MaayanLab/ChEA-KG-UI
Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries.
MaayanLab/datacrosswaysarchs4
MaayanLab/datadistillery-kg
MaayanLab/Enrichr-Viz-Appyter
Appyter for enrichr canvases, scatter plots, and Manhattan plots
MaayanLab/GenesToWordCloud
Remake of Genes2WordCloud
MaayanLab/hypothesispage
Simple hypothesis page, much simpler just to show PrismExp results
MaayanLab/KnowledgeGraphUIDemo
KnowledgeGraph Demo
MaayanLab/nbviewer
nbconvert as a web service: Render Jupyter Notebooks as static web pages
MaayanLab/postgrest-drs
A PostgREST powered DRS server
MaayanLab/RummageneXRummaGEO
MaayanLab/speedrichr