leahkemp
Computational biologist and data nerd. Also a pole dancer and heavy circle lifter.
Garvan Institute of Medical ResearchTaranaki, New Zealand
Pinned Repositories
human_genomics_pipeline
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
current_pipelines
A review of the current pipelines/tools available for analysing DNA/RNA data.
documentation
Documentation for various ESR projects.
ESR_human_genomics
An initial place to collate projects associated with the Human Genomics group at ESR
guinea_pore_c
Analysis documentation for part of the reference genome assembly of the humble guinea pig. Oxford Nanopore Technologies (ONT) pore-c data.
hyperparathyroid_analysis_20221102
Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.
ont_human_workflow
A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.
pipeface
Nextflow pipeline to align, variant call (SNP's, indels's, SV's) and phase long read ONT and/or pacbio HiFi data
RezBaz2020_snakemake_workshop
Snakemake workshop for RezBaz2020.
snakemake_workshop
Snakemake workshop
leahkemp's Repositories
leahkemp/current_pipelines
A review of the current pipelines/tools available for analysing DNA/RNA data.
leahkemp/documentation
Documentation for various ESR projects.
leahkemp/ont_human_workflow
A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.
leahkemp/RezBaz2020_snakemake_workshop
Snakemake workshop for RezBaz2020.
leahkemp/ESR_human_genomics
An initial place to collate projects associated with the Human Genomics group at ESR
leahkemp/nesi_A100s_parabricks_benchmarking
Benchmarking parabricks on NVIDIA A100's on NeSi.
leahkemp/running_16S_rRNA_pipeline
Trying to help a colleague get a 16s-rRNA-Sanger snakemake pipeline working.
leahkemp/smncrna_analysis_template
Small non-coding RNA analysis template for analysing Illumina small RNAseq data.
leahkemp/talks_etc
A place for talks, blurbs, bios etc related to work at ESR.
leahkemp/tasty_script_nibs
A collection of tasty script nibs I like and don't want to loose
leahkemp/test_SV_callers
Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).
leahkemp/guinea_pore_c
Analysis documentation for part of the reference genome assembly of the humble guinea pig. Oxford Nanopore Technologies (ONT) pore-c data.
leahkemp/hyperparathyroid_analysis_20221102
Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.
leahkemp/pipeface
Nextflow pipeline to align, variant call (SNP's, indels's, SV's) and phase long read ONT and/or pacbio HiFi data
leahkemp/adipose_ont_methylation
Analysis documentation for research into human adipose nanopore methylation. Oxford Nanopore Technologies (ONT), human, adipose, germline, adaptive sampling data.
leahkemp/assembly
Pipelines for assembling NGS data from Seattle flu study.
leahkemp/containers
Recipes for containerised software.
leahkemp/forensics_road_crashes_starter
A bit of starter code to help a colleague get started wrangling and extracting summary statistics from a road crash dataset in R.
leahkemp/hg_compute_resource_requirements
Minimal tests for the amount of compute resources required for analysing human genomics datasets at ESR.
leahkemp/leahkemp
leahkemp/madeline2_container
A simple singularity recipe for Madeline 2.0 Pedigree Drawing Engine.
leahkemp/ont_methylation
Adipose nanopore methylation project.
leahkemp/pipeline_wrapper_scripts
Wrapper scripts to automate some aspects of running human_genomics_pipeline and vcf_annotation_pipeline.
leahkemp/rna_analysis_template
Analysis template for analysing Illumina RNAseq data.
leahkemp/testing_seattleflu_assembly
Helping a colleague reviewing/testing the seattleflu/assembly pipeline.
leahkemp/training_plotting
Plotting my training data because I'm a nerd and a jock.
leahkemp/trevallyApp
An R Shiny app that presents a few key results of my MSc thesis.
leahkemp/welly-trevally
Files used to compile my MSc thesis.
leahkemp/welly-trevally-html
Files used to compile a gitbook version of my MSc thesis.