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bash_seq

This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.

bbtools-docker-singularity

Build Docker container for BBTools and (optionally) convert to Apptainer/Singularity.

bigwig

R interface to query UCSC bigWig files

bowtie2-docker-singularity

Build Docker container for Bowtie 2 and (optionally) convert to Apptainer/Singularity.

bwa-docker-singularity

Build Docker container for BWA and (optionally) convert to Apptainer/Singularity.

cld_docker

Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2

complexheatmap

Make Complex Heatmaps

cris.py

Analyze NGS data for CRISPR (or any engineered endonuclease) activity and screen for clones. Screen for NHEJ or multiple HDR events concurrently.

cytofbatchadjust

dreg

Detecting Regulatory Elements using GRO-seq and PRO-seq

dreg-model

Models used for running dREG

dtox

Identification of transcription factor binding patterns using genome-wide accessibility and transcription

eautils-docker-singularity

Build Docker container for ea-utils and (optionally) convert to Apptainer/Singularity.

ehahelper

Helper function for Event history analysis, including tidying functions for coxme

enrichedheatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

fastqc

A quality control analysis tool for high throughput sequencing data

fastqc-docker-singularity

Build Docker container for FastQC software and (optionally) convert to Apptainer/Singularity.

fastqscreen-docker-singularity

Build Docker container for FastQ Screen software and (optionally) convert to Apptainer/Singularity.

fastxtoolkit-docker-singularity

Build Docker container for FASTX Toolkit and (optionally) convert to Apptainer/Singularity.

fstitch

An algorithm to detect nascent RNA transcription in GRO-seq and ChIP-seq

ggpointdensity

:chart_with_upwards_trend: :bar_chart: Introduces geom_pointdensity(): A Cross Between a Scatter Plot and a 2D Density Plot.

gsea_r

Updated implementation of the GSEA-P R application for modern R distributions

hisat2-docker-singularity

Build Docker container for HISAT2 and (optionally) convert to Apptainer/Singularity.

homer-docker-singularity

Build Docker container for Homer software and optionally convert to Singularity/Apptainer for running on HPC system

htseq2-docker-singularity

Build Docker container for HTSeq and (optionally) convert to Apptainer/Singularity

include_examples

Example R scripts for analysis of INCLUDE data in CAVATICA

kids-first-elements-of-style-workflow-creation-maintenance

mds

Algorithms required to compute Motif Displacement Scores

memv3

Marker Enrichment Modeling v3

motif_displacement_analysis

A Python package for visualizing and exploring MD score computations