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rubin-cell-fate-conversion

Analysis scripts for the Rubin lab's cell fate conversion experiment

salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

salmon-cwl

Example CWL workflow for running Salmon

sambamba

Tools for working with SAM/BAM data

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scde

R package for analyzing single-cell RNA-seq data

schema_salad

Semantic Annotations for Linked Avro Data

seurat

R toolkit for single cell genomics

sickle

Windowed Adaptive Trimming for fastq files using quality

simdna

A python library for creating simulated regulatory DNA sequences

simple-rnaseq-sim

singlecell

single-cell data analysis incubator

singlecell-barcodes

whitelisted singlecell barcodes and information regarding where molecular/sample/cellular barcodes are in each read, for various singlecell protocols

sleuth

Inspect kallisto RNA-Seq output

slingshot

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

smrnaseq

A small-RNA sequencing analysis pipeline

spacemacs

Emacs advanced Kit focused on Evil: The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!

spacemacs-private

private layers for spacemacs

spliced-blog

data for the -spliced- blog

spp-idr

Wrappers around NGS peak callers to both call peaks and run IDR

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

tcrbiter

tcrbiter

test-transfer-repo

Testing if I can just transfer repositories to enterprise accounts

themetest

SinglePaged - Simple Jekyll template

tiny-test-data

Super small biological datasets for unit testing

titancna

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

toolz

A functional standard library for Python.

tophat-recondition

Post-processor for TopHat unmapped.bam files making them useable by downstream software.

training-modules

Materials for short, half-day workshops

transrate

Understand your transcriptome assembly