moqri

moqri's Stars

• jupyter/jupyter

  Jupyter metapackage for installation, docs and chat

  Language:Python14.8k6324014k

• satijalab/seurat

  R toolkit for single cell genomics

  Language:R2.2k757.7k892

• nglviewer/nglview

  Jupyter widget to interactively view molecular structures and trajectories

  Language:Jupyter Notebook79024487132

• aertslab/pySCENIC

  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

  Language:Python40018509176

• ParmEd/ParmEd

  Parameter/topology editor and molecular simulator

  Language:Python37533653148

• hbctraining/Intro-to-ChIPseq

  Intro to ChIPseq using HPC

  Language:SCSS2751070151

• DingWB/PyComplexHeatmap

  PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

  Language:Python25035828

• pinellolab/STREAM

  STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

  Language:Jupyter Notebook1691614645

• molgenis/systemsgenetics

  Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

  Language:Java1684793101

• Murali-group/Beeline

  BEELINE: evaluation of algorithms for gene regulatory network inference

  Language:Python167148451

• brentp/bwa-meth

  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

  Language:Python139137654

• guma44/GEOparse

  Python library to access Gene Expression Omnibus Database (GEO)

  Language:Jupyter Notebook13785850

• yupenghe/methylpy

  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

  Language:Python13158748

• nloyfer/wgbs_tools

  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

  Language:Python125116235

• ismms-himc/clustergrammer2

  "Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

  Language:HTML11347120

• cole-trapnell-lab/garnett

  Automated cell type classification

  Language:R99106324

• urmi-21/pyrpipe

  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

  Language:Python7871527

• xiaoyeye/CNNC

  covolutional neural network based coexpression analysis

  Language:Python7252523

• aertslab/arboreto

  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

  Language:Jupyter Notebook4963324

• padilha/biclustlib

  A Python library of biclustering algorithms, evaluation measures and datasets.

  Language:Python497218

• perishky/meffil

  Efficient algorithms for analyzing DNA methylation data.

  Language:HTML4995328

• Illumina/BeadArrayFiles

  Python library to parse file formats related to Illumina bead arrays

  Language:Python45191933

• brentp/combined-pvalues

  combining p-values using modified stouffer-liptak for spatially correlated results (probes)

  Language:Python4343322

• ismms-himc/clustergrammer2-notebooks

  Examples using Clustergrammer2 to explore high-dimensional datasets.

  Language:Jupyter Notebook404911

• liguowang/cpgtools

  Python package to analyze DNA methylation data

  Language:Python382710

• joshuagryphon/plastid

  Position-wise analysis of sequencing and genomics data

  Language:C3574816

• Christensen-Lab-Dartmouth/PyMethylProcess

  Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.

  Language:Python346168

• FoxoTech/methylprep

  Python-based preprocessing software for Illumina methylation arrays

  Language:Python3243414

• nicolerg/resources

  Documentation and tutorials worth sharing.

  Language:HTML10209

• marcrusso/DROPA

  DRIP Optimized Peak Annotator

  Language:Python5241