crinfante

rna-seq-lesson

A Carpentries-style lesson on RNA-Sequencing

decisionlabucsf.github.io

Decision Lab @ UCSF | neuroethics + decision neuroscience | led by Winston Chiong, MD PhD

transanno

accurate LiftOver tool for new genome assemblies

compleasm

A genome completeness evaluation tool based on miniprot

HiC_tools

A collection of tools for Hi-C data analysis

CenikLab.github.io

FLAG

deepTools

Tools to process and analyze deep sequencing data.

wiggleplotr

A small R package to make sequencing read coverage plots in R.

kent

UCSC Genome Browser source tree. Stable branch: "beta".

halLiftover-postprocessing

CUTandTAG

Analysis pipeline for CUT&TAG data

CUTTag_tutorial

Tutorial Website

Liftoff

An accurate GFF3/GTF lift over pipeline

canvasCourseCli

A Python-based command-line tool for retrieving, adding and updating content, pages and files exposed to students and teachers, for a Canvas instance (course)

styles

Official repository for Citation Style Language (CSL) citation styles.

human-rae-manuscript

code used for figure generation and statistical analysis for manuscript

steps2rr

Initial steps toward reproducible research (a minimal tutorial)

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

ruegg-et-al-wifl-genoscape

Code and data to reproduce results from Ruegg et al. paper on the Willow Flycatcher genoscape

how_we_work

Lab best practices and policies to conduct open, reproducible, and inspiring science that is efficient and fun

mackup

Keep your application settings in sync (OS X/Linux)

blobtoolkit

Interactive quality assessment of genome assemblies

syncthing

Open Source Continuous File Synchronization

mas

:package: Mac App Store command line interface

homebrew-bundle

📦 Bundler for non-Ruby dependencies from Homebrew, Homebrew Cask and the Mac App Store.

NicheMapR

R implementation of Niche Mapper software for biophysical modelling

LegoMicroscope

To learn about optics and microscopy, we generated a simple to build lego microscope that does not need precision optics and 3D printed parts.

RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

texture

A visual editor for research.