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code_aav_integrations

AAV integrations using RAAVioli in Ferrari, Jacob, Cesana et al, Cell Stem Cell

envd

🏕️ Reproducible development environment for AI/ML

gatk

Official code repository for GATK versions 4 and up

ggplot2

An implementation of the Grammar of Graphics in R

gsdensity

guideseq

Analysis pipeline for the GUIDE-seq assay. For news, see:

longampseq

The analysis for "CRISPR/Cas9 gene-editing of HSPCs from SCD patients has unintended consequences"

longread_umi

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

ot-review

Bioinformatics analysis for CRSIPR/Cas9 off-target review

pbbioconda

PacBio Secondary Analysis Tools on Bioconda

pbmm2

A minimap2 frontend for PacBio native data formats

practical-statistics-for-data-scientists

Code repository for O'Reilly book

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

r_toruloides

Scripts for Identification of Structrual Variants in R. touruloides

rhotermpredict

sc-type

scatac-seq_notes

scATAC-seq data analysis tools and papers

scppin

Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

scrna-seq

seurat

R toolkit for single cell genomics

seurat-wrappers

Community-provided extensions to Seurat

sniffles

Structural variation caller using third generation sequencing

structrual-variant-pipeline

unicycler

hybrid assembly pipeline for bacterial genomes