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nnlm

Nonnegative Linear Models (NNLM) and Nonnegative Matrix Factorization (NMF or NNMF).

nomeseq

The pipeline for NORM-Seq in tangfuchou lab for Epigenetic analysis.

northstar

Cell type annotation guided by cell atlases, with freedom to be queer

novosparc

omicsintegrator2

Prize-Collecting Steiner Forests for Interactomes

packagebuilder

paga

Mapping topologies of complex manifolds.

palimpsest

An R package for studying mutational and structural variant signatures along clonal evolution in cancer.

pancanstem_web

pcreode

An algorithm for mapping cell state transitions.

pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

peco

Predict cell cycle phase in a continuum in single-cell RNA-seq data analysis

perturbseq_gi

Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"

phemd

Package for comparing single-cell samples

phenograph

Subpopulation detection in high-dimensional single-cell data

pipeliner

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

plate_scatac-seq

A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method

poincaremaps

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

primate_cerebral_organoids

Scripts and functions achieve for the paper "Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development" (https://www.biorxiv.org/content/10.1101/685057v1)

projectr

propagate

:exclamation: This is a read-only mirror of the CRAN R package repository. propagate — Propagation of Uncertainty

propr

An R package to calculate proportionality between vectors of compositional data

prosstt

PRObabilistic Simulations of ScRNA-seq Tree-like Topologies

pseudodynamics

Dynamic models for single-cell RNA-seq time series.

psite

Simulate next-generation sequencing reads for tumor samples

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.

quack

Machine learning algorithm to predict biological pathway relationships based on functional genomics networks

r-style-guide

Best practices for readable, sharable, and verifiable R code

raceid3_stemid2_package

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and StemID2 method including novel functionalities and performance improvements compared to the previous RaceID3/StemID2 version in the RaceID3_StemID2 repository. The RaceID3_StemID2 repository will not be updated anymore in the future.

ragoo

Fast Reference-Guided Scaffolding of Genome Assembly Contigs