Alternatives and similar repositories for PENCIL:

Users that are interested in PENCIL are comparing it to the libraries listed below

• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 2 weeks ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆74Updated 4 months ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆46Updated 2 weeks ago
• lanagarmire / Asgard
  ☆42Updated last year
• yunguan-wang / SPROD
  SPROD: Spatial expression profiling de-noising
  ☆36Updated last year
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆58Updated last year
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆40Updated 3 months ago
• mcgilldinglab / scSemiProfiler
  A computational method scSemiProfiler that provides affordable single-cell data for large-scale disease cohorts using deep generative mod…
  ☆22Updated 3 weeks ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated last year
• xiaoyeye / TFvelo
  ☆43Updated last year
• madilabcode / scNET
  ☆41Updated 3 weeks ago
• snehamitra / SCARlink
  ☆50Updated 7 months ago
• WanluLiuLab / scAtlasVAE
  ☆34Updated 2 months ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆39Updated 3 years ago
• genecell / COSG
  Accurate and fast cell marker gene identification with COSG
  ☆44Updated last month
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆41Updated this week
• Roy-lab / scMTNI
  ☆26Updated 4 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated last year
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆61Updated 2 years ago
• axelalmet / flowsig
  Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.
  ☆73Updated 2 weeks ago
• AllonKleinLab / paper-data
  ☆20Updated this week
• theislab / neural_organoid_atlas
  Reproducibility repository for the Human Neural Organoid Atlas publication
  ☆32Updated 4 months ago
• Teichlab / Pan_fetal_immune
  Collection of scripts for analysis of pan fetal immune atlas
  ☆26Updated 2 years ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆26Updated this week
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• ZJUFanLab / scNiche
  a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution
  ☆26Updated 2 months ago
• ImmucanWP7 / immucan-scdb
  ☆16Updated last year
• ZJUFanLab / scRank
  A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gen…
  ☆46Updated 8 months ago
• ZJUFanLab / scSpace
  an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial tran…
  ☆22Updated last year