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apa

Used for Alternative Polyadenylation Analysis

bioconda-recipes

Conda recipes for the bioconda channel.

converters

different file format converters

cuhk-thesis-template

cuhkthesis

Latex thesis template for CUHK graduate students

cutqc

A simple wrapper for cutadapt and fastqc, and generate fastqc report with rmarkdown.

datasciencecoursera

emacs.d

An Emacs configuration bundle with batteries included

emacs.d-1

Efficient Emacs setup.

gitignore

A collection of useful .gitignore templates

log4j-detector

Scanner that detects vulnerable Log4J versions (CVE-2021-44228, CVE-2021-45046, etc) on your file-system within any application. It is able to even find instances that are hidden several layers deep. Works on Linux, Windows, and Mac, and everywhere else Java runs, too!

mirdp2_docker

Docker container for miRDeep-P2 miRNA identification pipline

miscs

nanom6a

obenno.r-universe.dev

parallel-fastq-dump

parallel fastq-dump wrapper

phas_discovery

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

scatac-seq

scATAC-seq pipeline based on nextflow

scrna-seq

scRNA-seq pipeline implemented with nextflow

scspotlight

A shiny app for single cell analysis based on Seurat

scspotlight_docs

Documentation website for scSpotlight, built with blogdown, hugo and relearn theme

shiny_blast

shinysyn

A shiny application to visualize MCscan result

soybean_salinity_ont_drs

Repo of scripts for analyzing soybean ONT DRS transcriptome under salt stress

starscope

ThunderBio scRNA-seq pipeline

trackcluster

An analysis pipeline for Nanopore direct-RNA sequencing

trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4

xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing