paulstothard
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sequence_manipulation_suite Public
A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for t…
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document-builder Public
Produces nicely formatted PDF and HTML documents from Markdown source files.
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helpful_links Public
Links to resources related to bioinformatics and data analysis.
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identify-shared-SVs Public
Identifies structural variant (SV) sites shared between two VCF files.
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Methods and scripts used to characterize chimeric mitochondrial RNA transcripts.
Python MIT License UpdatedSep 21, 2024 -
helpful_commands Public
Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks.
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A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.
Perl GNU General Public License v3.0 UpdatedJul 11, 2024 -
cgview Public
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
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sort_markdown_by_headings Public
Sorts a Markdown file based on headings.
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seq_to_json Public
Converts a raw, FASTA, GenBank, or EMBL file to a JSON file. Feature information is included in the output from GenBank and EMBL files.
Python GNU General Public License v3.0 UpdatedMay 1, 2024 -
ncbi_search Public
This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.
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cgview_comparison_tool Public
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
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fast-pptx Public
Generate Markdown and PowerPoint slides from a folder of images, code snippets, and other files.