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anchor

:anchor: Find bimodal, unimodal, and multimodal features in your data

bam_to_bigwig

A script to make stranded bigwig files from a bam file. Useful for STAMP edit C calculations.

bms_bioinformatics_bootcamp_2017

bodymap2

Flotilla package of Illumina bodymap data

bonvoyage

:triangular_ruler: Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.

chim-eclip

chimeric eCLIP processing pipeline

clip_analysis_legacy

clipper

A tool to identify CLIP-seq peaks

containers

Collection of Dockerfiles

cookiecutter-pypackage

Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.

craftid

software to accompany CRaftID paper

cred-portal-v2

cshl_2019

Course materials for CSHL 2019

cshl_2022

Collection of material to use for CSHL's Single Cell Analysis course 2022

cwl

CWL Documents for commandlinetools and workflows

eclip

eclip-qc

eclipdemux

demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)

expedition

Expedition suite for computing, visualizing, and analyzing single-cell alternative splicing data

f-shape-eclip

Generate fSHAPE/SHAPE reactivity profiles from (f)SHAPE-eCLIP reads.

flare

RNA edit detection (SAILOR) and peak calling (FLARE)

flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

flotilla_test_data

scrambled data for testing flotilla functionality

fshape

Generate fSHAPE reactivity profiles from in vivo/in vitro SHAPE probing reads.

gffutils

GFF and GTF file manipulation and interconversion

gscripts

General Use Scripts and Helper functions

hcp

Python port of Hierarchical Covariate with Prior from Matlab code

hydra

makebigwigfiles

Converts a BAM file into strand-specific bigwig files.

maketrackhubs