yuta-s79

yuta-s79's Stars

• zgyaru/testSctpa

  A portable toolkit for pathway activity score calculation

  Language:R86

• mckennalab/SingleCellLineage

  Updated scripts and pipelines for processing GESTALT data at single-cell resolution

  Language:Scala198

• lijxug/CSOmapR

  R package of CSOmap(developing

  Language:R144

• zhongguojie1998/CSOmap

  Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.

  Language:MATLAB64

• BiomedicalMachineLearning/stLearn

  A novel machine learning pipeline to analyse spatial transcriptomics data

  Language:Python19125

• bm2-lab/MUSIC

  model-based understanding of single-cell CRISPR screening

  Language:R2310

• shendurelab/single-cell-ko-screens

  Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hill, McFaline-Figueroa et al.

  Language:R2610

• Sun-lab/ideas

  Individual level Differential Expression Analysis for Single cells

  Language:R224

• yos-sk/nanoEM

  Codes for analysis of nanoEM data

  Language:Python5

• HeliXonProtein/OmegaFold

  OmegaFold Release Code

  Language:Python54676

• lbcb-sci/graphmap2

  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

  Language:C++666

• TheJacksonLaboratory/BRCA-LRseq-pipeline

  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

  Language:R144

• ay-lab/FitHiChIP

  Statistically Significant loops from HiChIP data

  Language:R3920

• andreariba/DeepCycle

  Cell cycle inference in single-cell RNA-seq

  Language:Python377

• plaisier-lab/U5_hNSC_Neural_G0

  Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma

  Language:R71

• YaqiangCao/cLoops

  Accurate and flexible loops calling tool for 3D genomic data.

  Language:Python11017

• vaquerizaslab/fanc

  FAN-C: Framework for the ANalysis of C-like data

  Language:Python10614

• saeyslab/nichenetr

  NicheNet: predict active ligand-target links between interacting cells

  Language:R470117

• GMichlits/CRISPR-UMI

  Repository for Publication "CRISPR-UMI: single-cell lineage tracing of pooled CRISPR–Cas9 screens" Michlits et al. Nature Methods 2017 Oct; 14: 1191-1197

  Language:Python1

• acayuelalopez/CellTypeAnalyzer

  :microscope: This is an ImageJ or Fiji plugin to identify, characterize, quantify and classify cells according to user-defined conditions.

  Language:Java10

• rnabioco/clustifyr

  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

  Language:R11214

• spundhir/idr

  Irreproducibility Discovery Rate analysis script

  Language:R32

• nboley/idr

  IDR

  Language:Python16645

• broadinstitute/Tangram

  Spatial alignment of single cell transcriptomic data.

  Language:Jupyter Notebook24950

• Irrationone/cellassign

  Automated, probabilistic assignment of cell types in scRNA-seq data

  Language:R19282

• bioinfo-tsukuba/CCPLS

  Language:R5

• KrishnaswamyLab/MAGIC

  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

  Language:Jupyter Notebook33897

• cozygene/bisque

  An R toolkit for estimation of cell composition from bulk expression data

  Language:R6820

• wanglabtongji/STRIDE

  STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using single-cell transcriptomics data.

  Language:Python174

• crazyhottommy/scRNAseq-analysis-notes

  scRNAseq analysis notes from Ming Tang

  630155