david-a-parry Goto Github PK

ese_finder

find ESE motifs

gatewayprimerdesigner

Simple tool to attempt automation of gateway cloning primer design

gene_coordinates_from_ucsc

genomeutils

Programs for simple but tedious genomic tasks - e.g. getting gene coordinates, retrieving DNA

getexonsfromucsc

Retrieves coordinates of exons from UCSC genome browser for a given gene

growth_calculator

het_hap_phaser

Phase haplotypes associated with a heterozygous variant

het_plotter

hts

biogo high throughput sequencing repository

indel_repeat_classifier

index_bam_by_read_id

python module for sorting, indexing and retrieving reads from BAMs using read IDs

indexbambyread

Perl module for indexing and retrieving BAM records by read ID

jacks

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

leafcutter

LeafCutter: Annotation-free quantification of RNA splicing. Yang I Li, David A Knowles, Jonathan K Pritchard.

mutationmapper

Predict functional consequences of mutations identified from sanger sequencing.

mutt

My mutt config files

muver

SNP and indel caller for mutation accumulation experiments

ora

orthologous residue annotator

panelapp_gene_scraper

Quickly scrape summary information from all gene entities from PanelApp

parse_vcf.py

ped_from_relatedness

Attempt to construct a simple PED file from relatedness statstics

perturbseq_workflow

Snakemake workflow for generating read count data from CRISPR screens.

powerlevel10k

A Zsh theme

random_football_score_generator

Randomly generate a set of football scores. Uses full time scores from English top 4 tiers between 1993-2018 to generate realistic scores.

rasp

Fork of RaSP repository from KULL-Centre/_2022_ML-ddG-Blaabjerg

recurseftp

retrieve or list files from an FTP site recursively in an automated fashion

region_finder

remove_vcf_info_fields

Remove one or more INFO fields from a VCF file

reverse

Rare Variant Enrichment and Recessive Segregation

sars-cov-2_oligos_vs_strains

Analysis of oligo vs SARS-COV2 strain sequences