Projects in Awesome Lists by gauravcodepro

https://github.com/sablokgaurav/graphanalyzer

graphanalyzer python package for dealing with paf and gfa alignments.

alignments bioinformatics genomes graphalignments graphs graphs-algorithms machinelearning

Last synced: 31 Jul 2025

https://github.com/gauravcodepro/ko-phylogenomics

analyzing bacterial genome based ontologies and phylogenomics informativeness

bacterial-genome-analysis bacterial-genomes geneontology genome-annotation ontologies ontology plant plantgenomes

Last synced: 02 Aug 2025

https://github.com/gauravcodepro/pangenome-single-copy-gene

a single copy gene analysis pangenome which allows for the orthology already computed and allows for the alignment and phylogeny building using three alignment approaches and also allows for the GTRCAT and GTRGAMA model with 1000 bootstrap. To check the file conversion it iterates the first files at the start and see if the number matches

bioinformatics bioinformatics-analysis pangenome pangenome-inference pangenome-pipeline

Last synced: 22 Jul 2025

https://github.com/gauravcodepro/pangenome-evolutionary

a complete workflow for analyzing the pangenomes from the core genesets. simply have to provide the fasta files and it will do everything and will make all the accessory information plots from the evolutionary analysis. It will also check for the breakage in the phylogeny and also will perform the repoint analysis.

bioinformatics evolutionary-computation evolutionary-computing pangenome pangenome-clustering pangenome-inference

Last synced: 04 Jul 2025

https://github.com/gauravcodepro/graph-sequence-similarity

a site specific function to estimate the site similarity across the graphs to make it faster, i implemented a linear approach so that it will compare the iterable as a list and then stores it in the another iterable. You can nest these functions as callables. Since graphs are nested as the linear in the grammar of the graphics

Last synced: 02 Aug 2025

https://github.com/gauravcodepro/go-hifi-profiler

profiling of the pacbiohifi reads, making mers and selective filtering of the mers for bubble pop

Last synced: 17 Jul 2025

https://github.com/gauravcodepro/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants

Last synced: 19 Jul 2025

https://github.com/gauravcodepro/pacbiohifi-read-assimilator

a pacbiohifi read check for the quick view of the read types.

fasta-sequences fastq-files genome-analysis hifi pacbio-data pacbio-sequencing pangenome

Last synced: 19 Jul 2025

https://github.com/gauravcodepro/condafetcher

a anaconda fetcher that interacts with the anaconda repository as a devops tool.

anaconda anaconda-distribution anaconda-environment anaconda3 conda conda-packages condapi devops devops-tools

Last synced: 11 Sep 2025

https://github.com/gauravcodepro/ontology-annotation-count

a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis

bacterial-genome-analysis bacterial-genomes genome genome-analysis genome-annotation genome-sequencing microbiome microbiome-analysis plantgenomes plantgenomics

Last synced: 20 Jul 2025

https://github.com/gauravcodepro/rnaprocessor

a python package processor for machine learning implementation of the target annotations and processing the transcriptomics for machine learning applications

Last synced: 26 May 2026

https://github.com/gauravcodepro/snp-extract

extracting all the snp sites for the panache and then estimating a identity matrix.

Last synced: 19 Jun 2025

https://github.com/gauravcodepro/devops-server

a ruby function to aid your devops for the sequencing reads and to run and generate the paths for the files for the entire sequencing reads cluster

bioinformatics cloud-computing cluster-computing devops ruby server-side-rendering

Last synced: 01 Aug 2025

https://github.com/gauravcodepro/visual-cloud-plots

a command line utility coded to incorporate all types of the plots for the single cell analysis plus incoporated some new ones. This will be updated regularly.After finishing all of the additions, I will add the shiny visualization also.

bioinformatics bioinformatics-analysis rprogramming single-cell-rna-seq singlecell-data-analysis singlecellgenomics

Last synced: 03 Aug 2025

https://github.com/gauravcodepro/genome-annotation-visualizer

a R function part to visualizae the genes coming from the genome alignment proteome annotations. This is a part of the evoseq R package

bioinformatics genome-alignment genome-annotation genome-assembly protein-sequences

Last synced: 08 Aug 2025

https://github.com/gauravcodepro/alignments-code-generator

a shell code getter for genomics alignments for the illumina and long reads from pacbio and the oxfordnanopore

illumina illumina-sequencing oxford-nanopore pacbio-data pacbio-hifi-sequencing-reads pacbio-sequencing

Last synced: 09 Aug 2025

https://github.com/gauravcodepro/proteinalignment-annotation-gem

a ruby gem for protein alignments. index the protein alignments, extract the regions of interest, extract the locus, extract the dimensions.

alignment-algorithm genome-annotation genome-browser protein-sequences proteinalignment proteins

Last synced: 14 Aug 2025

https://github.com/gauravcodepro/annotation-cleaner

A parallel encoded cluster computing Genome annotation cleaner that will take a genome annotation file and will clean them for the annotations and prepares for the machine learning

Last synced: 24 Aug 2025

https://github.com/gauravcodepro/sequence-annotation

A function to make the genome and the transcriptome annotations to reflect the gene regions and how they should be displayed. Provided a gff file and asked annotation and other columns it uses pygenomeviz to make all the annotation maps.

genome genome-analysis genome-annotation transcriptome-annotation

Last synced: 26 May 2026

https://github.com/gauravcodepro/tair-gff-ids

A set of functions which will provide easy access and cleaned gff from tair and uses a dataframe and datascience approach to get the systematic tair ids and their coordinates from the tair 10 gff version. It can be applied to any version of the tair for getting the systematic retrival of the tair ids.

genome genome-analysis genome-annotation genome-assembly genome-sequencing tair tair3 transcriptome-annotation transcriptome-assembly

Last synced: 05 Sep 2025

https://github.com/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

bioinformatics bioinformatics-pipeline bioinformatics-tool fungal-effectors fungal-genomes plantdisease plantdiseasedetection plantgenomics planthealth

Last synced: 06 Jul 2025

https://github.com/gauravcodepro/json-github

json parser for the github repository parse. Given the source code of the github it will make the direct clone address of the github reporitories.

configuration-files docker github github-pages kubernetes shell

Last synced: 28 Apr 2026

https://github.com/gauravcodepro/ensembl-plants

a single line code to resolve all the ensembl plants version and to make it usable for the genome assembly and further downstream analysis. Dont have to invoke the api access dicrectly and dont have to write a short::route connector

Last synced: 28 Aug 2025

https://github.com/gauravcodepro/diff-alternative-data-structure-r

I read this post today and they mentioned the diff which i have used a lot in R but i want to put this git just to show that you can also do this from a data structure point of view

data-science data-structures r rdataframe rprog rprogramming