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sip

SIP, a Single-cell Interchangeable Pipeline, still under construction

skylab

Secondary analysis pipelines

slicer

SLICER algorithm for inferring cell trajectories. See details in Welch et al., Genome Biology 2016: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0975-3

slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

snapatac

Single Nucleus Analysis Pipeline for ATAC-seq

snare_prep

dropseq-based single nuclei genomic accessibility and RNA expression (SNARE-seq) preprocessing pipeline

snrna-seq2_young

Analysis of snRNA-seq2 data coming from 3 months old mouse liver, dissecting the influence ploidy has on gene expression.

snvworkflow

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

souporcell

Clustering scRNAseq by genotypes

soupr

SOUP, for Semi-sOft clUstering with Pure cells.

split_index

Demultiplexes a fastq.

sscclust

simpler single cell RNAseq data clustering

steinernet

R Package: Steiner Tree Approach for Graph Analysis

steinernet-1

:exclamation: This is a read-only mirror of the CRAN R package repository. SteinerNet — Steiner Tree Approach for Graph Analysis. Homepage: https://github.com/krashkov/SteinerNet Report bugs for this package: https://github.com/krashkov/SteinerNet/issues

superfreq

Analysis pipeline for cancer exomes

swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

tabula_muris_networks

R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)

tangent

tcgabiolinks

TCGAbiolinks

template

A template Sphinx repo

texomer

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

tn_test

post-clustering differential expression test

topconfects

TOP results by CONfident efFECT Sizes.

topographer

trait

Source code and input data to reproduce the case studies presented in the TRaIT framework: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2795-4

treeexp

TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data

trinity_ctat

tximport

Import and summarize transcript-level estimates for gene-level analysis

ulcerative_colitis