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academic-kickstart

📝 Easily create a beautiful website using Academic, Hugo, and Netlify

al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

bedtools2

A powerful toolset for genome arithmetic.

bti

Bam Tag Index - Extract alignments from a bam file by tag

cellbrowser

Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

clustifyr

An R Package to cluster cell types from readcounts

cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cutadapt

Cutadapt removes adapter sequences from sequencing reads

deeptools

Tools to process and analyze deep sequencing data.

dplyr

Dplyr: A grammar of data manipulation

genomicfeatures

Conveniently import and query gene models

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

kentr

R package containing various tools for sequence analysis

lung-regeneration-meta

mpileup2readcounts

Get per-nucleotide readcounts from samtools mpileup

practical-data-analysis

Exploratory Data Analysis in R

rhtslib

HTSlib high-throughput sequencing library as an R package

rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

s4vectors

Foundation of vector-like and list-like containers in Bioconductor

scirnotebook

Template for building a lab notebook using RMarkdown

scrunchy

R toolkit for the analysis of single-cell functional heterogeneity

seurat

R toolkit for single cell genomics

tacorna.github.io

TACO Tool Website

toolbucket

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

valr

Genome interval arithmetic in R

valr-demo

Demonstrations of the valr package

variantannotation

Annotation of Genetic Variants

velocyto.py

RNA velocity estimation in Python