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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-module3-hollender

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

josephslab.github.io

latex-tutorial

A short tutorial on using LaTeX - a system for typesetting documents

merge-annotations-sequences

Merge a list of functional annotations with a fasta file of sequences

merge-fasta-lines

Merge each sequence in a multi-line fasta file onto individual lines

milesroberts-123.github.io

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

slurm-k-mer-gwas

k-mer-based GWAS on SLURM cluster

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

tajimasdacrossspecies

calculate genetic diversity within multiple species using both k-mer based and snp-based approaches

traitcorrelationcline

This repository contains all of the code for the analysis published here: XXX