biliopo

biliopo's Stars

• Zhen-Miao/PICsnATAC

  Paired Insertion Counting for snATAC-seq data

  Language:R151

• broadinstitute/Drop-seq

  Java tools for analyzing Drop-seq data

  Language:Java11934

• GreenleafLab/scScalpChromatin

  Language:R2211

• kundajelab/alzheimers_parkinsons

  Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

  Language:Jupyter Notebook4315

• whhudson/spatialTCR

  Language:HTML123

• kundajelab/Cardiogenesis_Repo

  Cardiogenesis Repo

  Language:Jupyter Notebook82

• helianfeixing/Zebrafish_scATAC

  Scripts and analysis of zebrafish embryo scATAC data.

  3

• KellisLab/AD_regulome_analysis

  AD regulome analysis

  Language:R101

• aertslab/iterative_peak_filtering

  Iterative peak filtering.

  Language:Shell44

• rasbt/machine-learning-book

  Code Repository for Machine Learning with PyTorch and Scikit-Learn

  Language:Jupyter Notebook3.3k1.2k

• prathyvsh/formal-systems-in-biology

  Application of formal systems to model biological systems

  46520

• fmicompbio/adv_scrnaseq_2020

  Material for lectures and exercises of the SIB course "Advanced topics in single-cell transcriptomics" (May 2020)

  Language:Jupyter Notebook179

• linnarsson-lab/fetal_brain_multiomics

  Supplementary files and notebooks to recreate figures.

  Language:HTML131

• Boyle-Lab/Blacklist

  Application for making ENCODE Blacklists

  Language:C++26136

• masai1116/SHARE-seq-alignmentV2

  Pipeline for demultiplexing and aligning both ATAC and RNA data generated in SHARE-seqV2

  Language:Python147

• aertslab/PUMATAC

  Pipeline for Universal Mapping of ATAC-seq

  Language:Nextflow201

• NBISweden/workshop-scRNAseq

  Single cell RNA sequencing analysis course

  Language:HTML19296

• DeplanckeLab/ChromatinHD

  High-definition modeling of chromatin + transcriptomics data

  Language:Python17

• czbiohub-sf/celltype_annotation_tutorial

  A repository for notebooks, figures, and utilities for cell-type annotation tutorial manuscript using CZ CELLxGENE ecosystem

  Language:Jupyter Notebook2

• AllenInstitute/scrattch.hicat

  Hierarchical, iterative clustering for analysis of transcriptomics data in R

  Language:HTML10631

• broadinstitute/epi-SHARE-seq-pipeline

  Epigenomics Program pipeline to analyze SHARE-seq data.

  Language:WDL173

• dpeerlab/SEACells

  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

  Language:Jupyter Notebook14426

• aertslab/scenicplus

  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

  Language:Jupyter Notebook17528

• AllonKleinLab/cospar

  Language:Python266

• haowenz/chromap

  Fast alignment and preprocessing of chromatin profiles

  Language:C++18820

• dyxmvp/spatial-CUT-Tag

  Language:R104

• seanken/CellLevel_QC

  A simple java based command to extract QC information (%intronic, %antisense, etc) from a CellRanger bam file.

  Language:Java7

• zentnerlab/STRIPE-seq

  Scripts and data files for exploration of STRIPE-seq data

  Language:R3

• seanken/FivePrime

  Code for our fiveprime RNASeq project

  Language:HTML12

• hz1010/FIPRESCI_data_analysis

  Code for FIPERSCI data

  Language:R2