milesroberts-123's repositories
slurm-k-mer-gwas
k-mer-based GWAS on SLURM cluster
tajimasDacrossSpecies
calculate genetic diversity within multiple species using both k-mer based and snp-based approaches
merge-annotations-sequences
Merge a list of functional annotations with a fasta file of sequences
arabidopsis-conditional-expression
Scripts associated with manuscript "Weaker selection on genes with treatment-specific expression may limit plasticity evolution in Arabidopsis thaliana"
cluster-motifs
Combine redundant motifs in a set of motifs
convert-bioprospector-to-transfac
Convert the output of BioProspector, the motif discovery algorithm, into a Transfac format that can be subsequently converted to MEME motif format
convert-blast-to-bed
Convert the output of BLAST to a BED file format that's suitable for uploading to JBrowse.
convert-dinamo-to-meme
Use regular expressions to convert the motifs output by DiNAMO into true MEME motif format
convert-fimo-to-instances
Take the list of motif occurrences output by FIMO (a MEME suite tool) and convert it into the Instances format used by MotifSuite tools.
convert-hdf5-to-text
Convert the data in a hdf5-formatted file into a series of text files, which are easier to manipulate.
convert-homer-to-meme
Use regular expressions to convert a list of motifs in HOMER format to MEME motif format
convert-motifsuite-to-meme
Use regular expressions to convert the PWM-format used by MotifSuite to MEME motif format.
convert-prosampler-to-meme
Use regular expressions to convert the motifs output by ProSampler to MEME motif format.
CSS844_module2
Extract phenotypes from Syngenta corn pictures
dndscount
Simple counting methods for calculating dN/dS for pairwise codon-based alignment of genes in species pairs
extract-annotations
Use Biopython to extract functional gene annotations from a GFF file and output them as a tab-delimited text file.
extract-sequence-lengths
Extract sequence lengths from a fasta file and save them to a tab-delimited text file in genome file format.
extract-sequence-sets
Extract multiple sets of sequences, mutually exclusive or not, from a single fasta file.
extract-weird-proteins
Remove proteins that have internal stop codons and/or do not begin with methionine from a fasta file.
fry-taste-test
Roberts et al 2024 study of which frozen french fry is the best
LaTeX-tutorial
A short tutorial on using LaTeX - a system for typesetting documents
merge-fasta-lines
Merge each sequence in a multi-line fasta file onto individual lines
remove-sequences
Remove sequences from one fasta file that match names of sequences in another fasta file
selection-demography-cnn
A workflow to train a convolutional neural network with SLiM outputs
snakemake-aks-tutorial
This is a record of my efforts to get snakemake to run on Azure Kubernetes Service. Works as of 2023-01-31
snakemake-tutorial
A brief and simple snakemake tutorial
TraitCorrelationCline
This repository contains all of the code for the analysis published here: XXX