raymondkiu

bactspeciesID

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

binary_tree

To convert gene-presence-absence matrix into multi fasta alignment

bioinformatics-tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

blastoutput2gff

Convert BLAST output (tabular format 6) to gff format for sequence extraction using bedtools

bracken-filter-reads

This script filters low abundant reads from Bracken outputs for downstream analyses

eggnog-mapper_COGextraction

Extraction of COG functional classes and save the data in csv format

fastq-info

Calculate fastq reads and sequencing coverage

fqtk

fqtk: A toolkit to perform common tasks on FASTQ reads. Rename FASTQ identifiers, print FASTQ statistics and convert FASTQ to FASTA. This program is written in AWK and Bash.

R-scripts-graphing-statistics

My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

sequence-stats

Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

raymondkiu/bioinformatics-tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

raymondkiu/fastq-info

Calculate fastq reads and sequencing coverage

raymondkiu/sequence-stats

Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

raymondkiu/R-scripts-graphing-statistics

My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

raymondkiu/bactspeciesID

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

raymondkiu/bracken-filter-reads

This script filters low abundant reads from Bracken outputs for downstream analyses

raymondkiu/binary_tree

To convert gene-presence-absence matrix into multi fasta alignment

raymondkiu/eggnog-mapper_COGextraction

Extraction of COG functional classes and save the data in csv format

raymondkiu/fqtk

fqtk: A toolkit to perform common tasks on FASTQ reads. Rename FASTQ identifiers, print FASTQ statistics and convert FASTQ to FASTA. This program is written in AWK and Bash.

raymondkiu/16S_extraction_Barrnap

Automated 16S sequence extraction using Barrnap output gff files

raymondkiu/fastq_reads

Count fastq reads

raymondkiu/Genome-extraction-metagenome

Extracting single genome from a complex metagenome using reference based approaches

raymondkiu/Infant-Clostridium-perfringens-Paper

Source data files and sequence databases used in the paper

raymondkiu/Plotting

R scripts for routine plotting tasks

raymondkiu/R-stats

Statistical testing using R packages - various examples great for R beginners.

raymondkiu/TOXIper

Toxinotype assignment of Clostridium perfringens via ABRicate

raymondkiu/Bifidobacterium-IEC-transcriptomics

Codes used to analyse RNA-Seq data

raymondkiu/cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

raymondkiu/databases

My personal sequence databases

raymondkiu/Food-poisoning

raymondkiu/genomesizebp_fasta

Compute genome size of fasta assemblies

raymondkiu/Infant-Resistome-Study

Source data files (also R scripts) used in the paper

raymondkiu/Maternal-foetal-microbiota-paper

Scripts for differential gene expression analysis

raymondkiu/meanPhredScore

raymondkiu/printProkkaStats

Print a table of Prokka annotation stats (output .txt)

raymondkiu/raymondkiu.github.io

My website

raymondkiu/reference

raymondkiu/reverse_complement_nucleotide

To compute reverse complement of nucleotide sequences

raymondkiu/Thesis

Data generated in my thesis in 2018

raymondkiu/vertical_horizontal

To convert vertical text into horizontal text with spacing in between.