stepbystep99

stepbystep99's Stars

• satijalab/seurat

  R toolkit for single cell genomics

  Language:R2.3k738k915

• scverse/scanpy

  Single-cell analysis in Python. Scales to >1M cells.

  Language:Python1.9k511.8k602

• KlugerLab/FIt-SNE

  Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

  Language:C++5923675108

• broadinstitute/infercnv

  Inferring CNV from Single-Cell RNA-Seq

  Language:R56540585166

• 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 Notebook3452214397

• hms-dbmi/scde

  R package for analyzing single-cell RNA-seq data

  Language:R173258166

• molgenis/systemsgenetics

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

  Language:Java1714794100

• colomemaria/epiScanpy

  Episcanpy: Epigenomics Single Cell Analysis in Python

  Language:Python14145232

• broadinstitute/wot

  A software package for analyzing snapshots of developmental processes

  Language:Jupyter Notebook140128234

• TrinityCTAT/Trinity_CTAT

  11527334

• livnatje/ImmuneResistance

  This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".

  Language:R727944

• neurogenomics/MAGMA_Celltyping

  Find causal cell-types underlying complex trait genetics

  Language:R71514131

• MarioniLab/EmbryoTimecourse2018

  Data and analysis scripts for our Embryo Timecourse paper.

  Language:HTML6561035

• sandhya212/BISCUIT_SingleCell_IMM_ICML_2016

  R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

  Language:R65123133

• NathanSkene/EWCE

  Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

  Language:R5458625

• KlugerLab/t-SNE-Heatmaps

  Beta version of 1D t-SNE heatmaps to visualize expression patterns of hundreds of genes simultaneously in scRNA-seq

  Language:R489111

• Japrin/sscClust

  simpler single cell RNAseq data clustering

  Language:R403517

• linnarsson-lab/cytograph

  Algorithms for single-cell analysis

  Language:Python29215

• pachterlab/NYMP_2018

  Language:Jupyter Notebook291869

• rajewsky-lab/planarian_lineages

  Language:Jupyter Notebook25657

• AllenInstitute/tasic2018analysis

  Scripts related to VISp and ALM scRNA-seq and FISH analysis for Tasic, et al., 2018.

  Language:R24603

• tinglab/reCAT

  Language:R202159

• molgenis/scRNA-seq

  Language:HTML181445

• mm-shah/MetaNeighbor

  A method to rapidly assess cell type identity using both functional and random gene sets

  Language:R143211

• KafsackLab/scRNAseq-Malaria

  Codes associated with the Poran, Nötzel et al. paper titled "Single-cell RNA-seq reveals a signature of sexual commitment in malaria parasites".

  Language:R10007

• Castelo-Branco-lab/GeneFocus

  Network-based spatial clustering on diffusionmaps

  1202

• stepbystep99/awesome-single-cell

  List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

  1100

• stepbystep99/Deconvolution2016

  Code and manuscript files for Aaron and Karsten's deconvolution paper.

  Language:TeX1100

• stepbystep99/Lineage

  1100

• stepbystep99/PBA

  Population balance analysis

  Language:Python1100