TealFurnholm/Universal_Biological_Reactions_Database

A compiled and cross-id mapped enzymatic database with reaction direction, product and reactant compounds.

Size: 1.95 KB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

TealFurnholm/Strain-Level_Metatranscriptome_Analysis

Directly align reads to a universal reference database. Use the whole community and uniquely mapping reads -> unique genes to clean-up matching. Get quantitative and comparable community phylogenies, genes, and functions.

Language: Perl - Size: 36.1 KB - Last synced: 8 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 1

TealFurnholm/UMRAD

Universal Multi-omics Reference and Alignment Database

Language: Perl - Size: 147 KB - Last synced: 8 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 3

TealFurnholm/Universal-Taxonomy-Database

Lineages of all organisms and vectors curated to conform with taxonomic conventions creating a clean, untangled phylogentic tree to the strain-level. Use for generating "lowest common ancestor" in meta-omics/next-generation sequencing.

Language: Perl - Size: 4.45 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 2

TealFurnholm/Meta-omics_Functional_Analysis

Quantify and compare biosynthetic and immunological functions-pathways in your microbial community using a variety of key words and functional ids.

Size: 8.95 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

TealFurnholm/Muscato

Muscato Alignment Software Benchmarking

Language: HTML - Size: 83 KB - Last synced: 8 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

TealFurnholm/eddefyjs Fork of JoyceBettencourt/eddefyjs

Size: 375 KB - Last synced: 8 months ago - Pushed: about 11 years ago - Stars: 1 - Forks: 1

TealFurnholm/Helpful_Scripts

Language: Perl - Size: 2.93 KB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

TealFurnholm/Fix_RNACentral_Taxonomy

Uses curated taxonomy and various software to clean up and deduplicate RNAcentral's database

Language: Perl - Size: 4.88 KB - Last synced: 8 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

TealFurnholm/Community-Based-Metagenome-Binning

Uses my Universal Reference Database and the ContigAnalysis.pl output to generate functionally complete strain-specific MAGs.

Size: 1.95 KB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

TealFurnholm/Universal_Biological_Compounds_Database

This script compiles and links biological reactions and compound information from across multiple public repositories.

Language: Perl - Size: 73.2 KB - Last synced: 8 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 2

TealFurnholm/Fix-SILVA-SSU-taxonomy

Use my curated taxonomy database to get standardized lineages for the SILVA SSU genes

Language: Perl - Size: 6.84 KB - Last synced: 8 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

TealFurnholm/Strain-Level_Metagenome_Analysis

Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.

Language: Perl - Size: 821 KB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

TealFurnholm/Universal_Microbiomics_Alignment_Database

Align sequencing reads or peptides to this modified and heavily curated UniRef database to get simultaneous quantitative community phylogeny and functions.

Language: Perl - Size: 35.2 KB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1