Pinned Repositories
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
computational-statistics
Methods for computational statistics. Optimization, EM, MCMC, Bayesian Modeling, Variational inference.
datasharing
The Leek group guide to data sharing
GVCF_pipeline-nf
Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment
hernet.github.io
jz-native-mobile-apps
Native JavaZone apps for Android and iOS
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.
SAUCIE
scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
transcriptional-map-nk
We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and tissue. We also analyze data from various solid tumors and map these onto this reference.
hernet's Repositories
hernet/transcriptional-map-nk
We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and tissue. We also analyze data from various solid tumors and map these onto this reference.
hernet/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
hernet/computational-statistics
Methods for computational statistics. Optimization, EM, MCMC, Bayesian Modeling, Variational inference.
hernet/datasharing
The Leek group guide to data sharing
hernet/GVCF_pipeline-nf
Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment
hernet/hernet.github.io
hernet/jz-native-mobile-apps
Native JavaZone apps for Android and iOS
hernet/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.
hernet/SAUCIE
hernet/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
hernet/scVI
Deep generative modeling for single-cell transcriptomics
hernet/seqc
Single-Cell Sequencing Quality Control and Processing Software
hernet/SingleFlow
SingleFlow is a pipeline for analyzing scRNA-seq data.
hernet/trVAE
Conditional Out-of-Sample prediction
hernet/txpp
Pipeline for preprocessing of scRNA-seq 10x genomics FASTQ files. Produces loom files with counts of spliced and unspliced transcripts (for RNA velocity computation) as well as an expression count matrix.