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scrnaaltas_tnbc_mm

scrnaseqworkflow

Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz

scsa

SCSA: cell type annotation for single-cell RNA-seq data

scvi

Deep generative modeling for single-cell transcriptomics

seurat-wrappers

Community-provided extensions to Seurat

shinygeo

Gene Expression Omnibus Analysis with Shiny :microscope:

simlr

Implementations in both Matlab and R of the SIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/nmeth.4207

single-cell-rnaseq-analysis

A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, custom visualizations, and group-wise analysis of tumor infiltrating immune cells using data from Ishizuka et al. Nature 2019.

singlecell_bcatlas

Breast Cancer Single Cell Atlas

singlecellhaystack

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

sleuth

Differential analysis of RNA-Seq

snapatac

Single Nucleus Analysis Pipeline for ATAC-seq

snaptools

A module for working with snap files in Python

sparsedc

:exclamation: This is a read-only mirror of the CRAN R package repository. SparseDC — Implementation of SparseDC Algorithm

spectralnet

Deep network that performs spectral clustering

star

RNA-seq aligner

stemid

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.

suppa

SUPPA2: Fast quantification of differential splicing

switchde

Inference of switch-like differential expression along single-cell trajectories

t-sne-java

Pure Java implementation of Van Der Maaten and Hinton's t-sne clustering algorithm

t-sne-tutorial

A tutorial on the t-SNE learning algorithm

teachingmaterial

RNA-seq data analysis practical

tenx

Pipelines for the analysis of 10x single-cell RNA-sequencing data

testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.

tflearn-vae

tflearn implementation of variational autoencoder

tools

Python package with helper tools for the nf-core community.

tpmcalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

tsescore_icis

Calculate the TSE score to predict response to ICIs

tsne

A python wrapper for Barnes-Hut tsne

tybalt

Training and evaluating a variational autoencoder for pan-cancer gene expression data