Ecosyste.ms: Repos
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GitHub topics: fungal-genomes
gauravcodepro/plant-resistance_gene_isolator
I coded this function to make a comprehensive gene isolation for the plant resistance genes from the long reads sequencing. Given PacBio or Oxford Nanopore Reads, it will assemble, predict the plant disease resistance genes and will allow you to analyze the mutations in the plant disease resistance genes
Language: Shell - Size: 480 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/fungal-ITS-coverage-calculator
I coded this function to estimate the fraction of the ITS predictions from the fungal metagenomics and it estimates by taking into account the sequence length and also the ITS1 and ITS2 start and stop coordinates. Provided a keyworded argument, it estimates the coverage accordingly
Language: Python - Size: 42 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/evolutionary-rate-analyer
A R function for the analysis of the evolutionary rates from the fasta files, and uses the ka/ks and the dn/ds and plots the evolutionary rates.
Language: R - Size: 9.77 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/langchain-candida-literature-miner
This prepares the candida literature for the machine learning. Although prepared for candida, it can be used for any specific term that you want to search in pubmed
Language: Python - Size: 121 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 1
gauravcodepro/ontology-network-candida
A faster implementation of the gene ontology analyzer for the candida genomes, given the candida go ontology files and a search GO term, it extracts all the alt_id, relationship_ids and associated function with those gene ontology for the network analysis and to link with the expression analysis.
Language: Python - Size: 42 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/miseq-nextseq-novaseq-genome
shell assembler that takes only the directory path and does all the cleaning of the reads, mapping, remapping and assembly. From start to finish everything by providing a simple directory path.
Language: Shell - Size: 27.3 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/domain-analyzer
This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. I used a mapping dataframe approach to make it faster rather than looping it over and over.
Language: Python - Size: 64.5 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
lakhanp1/fungal_resources
R AnnotationDB resources like org.db, tx.db for various fungal species
Language: R - Size: 196 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 2
sablokgaurav/plant_long_read_resistance_gene_variant_estimator
This contains a complete workflow for the estimation of variant estimators from the long reads and it estimates using the NBS LRR specific resistance genes.
Language: Shell - Size: 668 KB - Last synced: 4 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
sablokgaurav/fungal_genome_evolution
fungal_genome_evolution
Size: 1000 Bytes - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0