Repositories list

• immune-knowledgegraph.github.io

  Public
  Python

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• Monopogen

  Public
  SNV calling from single cell sequencing

  somatic-variantssingle-cellsnvs+ 1germline-variants

  HTML

  •

  GNU General Public License v3.0

  •18•85•43•1•Updated Nov 11, 2024Nov 11, 2024

• transition-cells-identification

  Public
  Jupyter Notebook

  •

  MIT License

  •1•2•0•0•Updated Nov 2, 2024Nov 2, 2024

• SCMER

  Public
  Marker Selection by matching manifolds and elastic net

  feature-selectionsingle-cell-analysis

  HTML

  •

  MIT License

  •4•23•0•0•Updated Oct 22, 2024Oct 22, 2024

• INVAX_manuscript

  Public
  Scripts/Codes for INVAX project paper

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 19, 2024Oct 19, 2024

• LSGI

  Public
  HTML

  •3•1•0•0•Updated Sep 6, 2024Sep 6, 2024

• METAFlux

  Public
  HTML

  •

  Other

  •9•48•14•0•Updated Jun 29, 2024Jun 29, 2024

• lad

  Public
  Visualization and analysis of single-cell RNA-seq data by alternative clustering

  Jupyter Notebook

  •2•0•0•0•Updated Feb 11, 2024Feb 11, 2024

• bcd

  Public
  Visualization and analysis of single-cell RNA-seq data by alternative clustering

  statistical-methodssingle-cellbatch-effects

  HTML

  •2•4•1•0•Updated Nov 23, 2023Nov 23, 2023

• NK_CEBPD_manuscript

  Public
  Scripts/Codes for NK CEBPD paper

  R

  •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

• MEDALT

  Public
  Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile

  R

  •

  MIT License

  •2•17•6•0•Updated Sep 8, 2023Sep 8, 2023

• bindSC

  Public
  Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data

  integrative-analysissingle-cell-analysis

  R

  •

  GNU General Public License v3.0

  •7•34•2•0•Updated Aug 23, 2023Aug 23, 2023

• MCL_ML_Project

  Public
  Code for models and visualizations for HHill's MCL ML project.

  Jupyter Notebook

  •1•0•0•0•Updated May 10, 2023May 10, 2023

• Data-Analysis-of-Variant-Functional-Effects

  Public
  Data analysis for manuscript submission

  R

  •

  MIT License

  •0•0•0•0•Updated Apr 25, 2023Apr 25, 2023

• novoRNABreak

  Public
  Perl

  •

  MIT License

  •0•0•0•0•Updated Mar 21, 2023Mar 21, 2023

• gsdensity

  Public
  HTML

  •2•9•1•0•Updated Mar 12, 2023Mar 12, 2023

• CCAdge

  Public
  Detection of disease-associated genes from single cell data

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 4, 2023Jan 4, 2023

• epiNB

  Public
  Efficient and interpretable HLA-I binding peptide identification

  Pep8

  •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

• Cyclum

  Public
  Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations

  single-cell-rna-seqartifical-neural-networktrajectory-inference-methods+ 1latent-process-inference

  Python

  •

  MIT License

  •4•20•1•0•Updated Dec 17, 2021Dec 17, 2021

• sensei

  Public
  Sample size estimation for single cell studies

  single-cell-analysissample-size-calculationstudy-design+ 1beta-binomial

  HTML

  •

  MIT License

  •0•0•0•0•Updated Nov 18, 2021Nov 18, 2021

• stratified-tests-for-seurat

  Public
  Stratified statistic hypothesis tests for Seurat

  HTML

  •

  GNU General Public License v3.0

  •2•6•0•0•Updated Nov 8, 2021Nov 8, 2021

• CytoSpill

  Public
  A statistical approach that reduces spillover noise in the mass cytometry (CyTOF) data

  R

  •6•2•4•2•Updated Apr 30, 2021Apr 30, 2021

• Cyclum-GP

  Public
  A more flexible version of Cyclum, utilizing GPLVM with periodic kernel

  Jupyter Notebook

  •0•0•0•0•Updated Dec 27, 2020Dec 27, 2020

• SCMarker

  Public
  Marker gene selection from scRNA-seq data

  statistical-methodshigh-dimensional-datafeature-selection+ 1single-cell-rna-seq

  HTML

  •2•15•2•0•Updated Sep 15, 2020Sep 15, 2020

• Texomer

  Public
  Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

  statistical-inferencefunctional-variantstcga-data+ 1tumor-heterogeneity

  R

  •8•20•3•1•Updated Aug 19, 2020Aug 19, 2020

• MonoVar

  Public
  Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

  variant-callingsingle-cell-dna-seq

  Python

  •7•11•3•1•Updated May 8, 2020May 8, 2020

• Cyclum-Demo

  Public
  A self-contained demo of Cyclum, ships with the mESC data

  Python

  •2•0•0•0•Updated Feb 18, 2020Feb 18, 2020

• tf-rna-atac

  Public
  Clustering transcription factors based on expression and chromatin openness

  HTML

  •

  MIT License

  •1•0•0•0•Updated Jan 28, 2020Jan 28, 2020

• SiFit

  Public
  Reconstructing phylogenetic tree from noisy mutation profile of single cells

  phylogenetic-treescancer-genomicssingle-cell-genomics+ 1tumor-heterogeneity

  Other

  •2•3•3•0•Updated Jul 4, 2019Jul 4, 2019

• TransVar

  Public
  A multi-way annotator for genetic elements and genetic variations

  protein-sequencesrna-transcriptionfunctional-annotation

  Python

  •

  Other

  •0•1•1•0•Updated Dec 11, 2018Dec 11, 2018