Pinned Repositories
assembly_stats
A simple script to calculate some basic assembly statistics
bioconda-recipes
Conda recipes for the bioconda channel.
blast_parsing
A couple scripts to parse BLAST output and retrieve the target sequences
create_microscopy_probes
Creates unique DNA probes and their primers for FISH microscopy
create_pcr_primers
A script to make PCR primers going off the end of a contig (i.e. to circularize it)
CSI
DeepMod
DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
deepTools
Tools to process and analyze deep sequencing data.
egg_simulation
A simulation of Hodgkinia transmission in cicadas
remove_orphan_reads
A script to take two fastq files and split them by reads that are paired and those that are unpaired
mattsoup's Repositories
mattsoup/remove_orphan_reads
A script to take two fastq files and split them by reads that are paired and those that are unpaired
mattsoup/assembly_stats
A simple script to calculate some basic assembly statistics
mattsoup/bioconda-recipes
Conda recipes for the bioconda channel.
mattsoup/blast_parsing
A couple scripts to parse BLAST output and retrieve the target sequences
mattsoup/create_microscopy_probes
Creates unique DNA probes and their primers for FISH microscopy
mattsoup/create_pcr_primers
A script to make PCR primers going off the end of a contig (i.e. to circularize it)
mattsoup/CSI
mattsoup/DeepMod
DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
mattsoup/deepTools
Tools to process and analyze deep sequencing data.
mattsoup/egg_simulation
A simulation of Hodgkinia transmission in cicadas
mattsoup/helpful_scripts
Just some common, useful scripts / functions I use frequently
mattsoup/hodgkinia_model
A model for hodgkinia and symbionts
mattsoup/MethylDackel
A (mostly) universal methylation extractor for BS-seq experiments.
mattsoup/methylKit
R package for DNA methylation analysis
mattsoup/MiniProject
A little project I did to visualize sequencing coverage
mattsoup/read_mapping_figure
Python and Processing (python mode) scripts to map reads on a circular contig
mattsoup/simple_checkers
mattsoup/six_frame_translate
Translates a nucleotide fasta file in all six reading frames