Projects in Awesome Lists by gauravcodepro

https://github.com/gauravcodepro/pangraphs-genome-assembly

genome assembly to pangraphs from illumina to long reads.

bioinformatics container-image containerization docker longread pacbio-data pacbio-iso-seq pacbio-sequencing

Last synced: 18 Mar 2025

https://github.com/gauravcodepro/genome-shell-utility

a genome shell utility to help you with the project management and organization. It will automatically create the folders and transfers the files to the sever and will move around.

clusters genome genomeutility hpc-clusters server

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/genomic-alignment-extraction

A scalable large scale genomic fraction aligner and extractor for the large scale alignment of the genomes and the transcriptomes and process them over the cores for the extraction of the aligned regions. The aligned regions can also be mapped to the length plotter and can be machine trained for specific applications

alignment-algorithms alignmentextract alignments genome genome-annotation genome-assembly genomealignment transcriptome-analysis transcriptomealignment transcriptomics

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/plant-microarray-analysis

analysis of already normalized microarray expression profiles and perform batch analysis and plots the volcano plots and differential expression

microarray microarray-analysis microarray-data-analysis microarray-experiments

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/graphanalyzer

graphanalyzer python package for dealing with paf and gfa alignments.

alignments bioinformatics genomes graphalignments graphs graphs-algorithms machinelearning

Last synced: 26 Feb 2025

https://github.com/gauravcodepro/tair-pubmed-connector

There is no function to fetch automatically the information on the reported pubmed articles links in the tair to be used for the language models, so i coded this function which will take the tair information, a gene or locus tag and will fetch the corresponding pubmed and then from the pubmed the corresponding abstracts

bioinformatics bioinformatics-analysis bioinformatics-tool genome-annotation language-model pubmed pubmed-abstracts pubmed-articles-grabber pubmed-records tair3

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pangenomes-metagenomes

a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads

bacterial-genomes bioinformatics metagenomes metagenomics-data pangenomics pangraphs

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/genome-size-estimation

a genome reference estimation based on the peak size calibration and the given the values of the peak size calibration will estimate the genome and the sub genome fraction.

genome genome-analysis genome-assembly genome-sequencing size-calculation size-optimization

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/langchain-candida-literature-miner

candida literature bert machine learning. works on any literature term from pubmed.

fungal-genomes fungalgenomics machinelearning natural-language-generation natural-language-processing pubmed pubmed-abstracts pubmed-records

Last synced: 26 Feb 2025

https://github.com/gauravcodepro/pubmed-abstract-fetcher

This function will prepare the abstract and the id information for all the pubmed articles that you want to read and have as a citation. I coded this using a web scraping approach and it is blazing fast and parses better than ncbi eutils

bioinformatics corpus genomics language-model language-modeling natural-language-processing pubmed pubmed-parser

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/protein-annotator

python package to analyze the protein coding regions for the genome annotation. It uses the miniprot for the alignment and gives you all the protein predicted mRNA, coding regions and other exon positions.

bioinformatics genome-alignment genome-analysis genome-annotation protein-sequences python-library

Last synced: 22 Feb 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 Feb 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: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/tairaccession

tairaccession python package for interaction with tair and analyzing arabidopsis genome.

annotation-processor annotation-tool arabidopsis bioinformatics bioinformatics-tool comparative-analysis comparative-genomics genome-analysis genome-annotation phytozome plantgenomes plantgenomics tair3

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/nextflow-pacbiohifi

a nextflow pacbiohifi for the genome assembly from the pacbiohifi

bioinformatics nextflow nextflow-language nextflow-pipeline nextflow-process pacbio-data pacbiohifi

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/python-datastructures

python datastructure and algorithms

codewars codewars-kata codewars-kata-solution codewars-solutions datastructures datastructures-algorithms faang-interview interview interview-preparation interview-questions leetcode-python leetcode-questions leetcode-solutions

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pacbio-nanopore-repeat-coverage

a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly

bioinformatics bioinformatics-algorithms bioinformatics-tool longread oxford-nanopore pacbio pacbio-sequencing sequencing-coverage sequencing-data sequencing-error

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/numpy-builder

A numpy shell builder to extract and how to use the numpy across the arrays.I am putting the entire manual for those who like to search immediately rather than looking here and there.

bash-prompt bash-script bash-scripting data-analysis data-mining data-science numpy numpy-arrays shell-prompt shell-script

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/genome-analysis-slurm-pbs

slurm and pbs scripts for genome, metagenome, transcriptome analysis.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomic-data-analysis genomics genomics-visualization

Last synced: 22 Feb 2025

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: 05 Dec 2024

https://github.com/gauravcodepro/codingplotter

a coding plotter for the protein annotations coming from the annotation of the genome using the protein hints and to extract and plot the specific length estimates.

bioinformatics bioinformatics-visualization genome-analysis genome-annotation protein-sequences

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/visualize-proteins

a protein visualization for the annotation of the genome transcripts and their integration into the genome maps. You can have the alignments in any gfa, mfa or paf format and it will visualize the transcripts to the gene alignments.

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/zenity-docker-nu

a zenity app for the docker subnet masking check with nu rust programming. I coded this earlier also for slurm and pbs and now put it for the docker also. you can define your docker processid and it will get the netmask for the same so that you can connect to those instances easily. I coded this for the slurm and pbs cluster

cluster-computing docker nushell nushell-core nushell-script

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/zsh-posh-scrap

ZSH_POSH_web_scrapping: This repository contains the bash based web scrapping if you want to install the nerd fonts for programming

bash bash-scripting font-awesome fonts nerd-fonts oh-my-posh oh-my-posh-theme oh-my-zsh-theme programming programming-fonts webscraping

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/transdecoder-visualization

a regular expression based trinity assembly transdecoder predictions encoder which will parse and will prepare the transcript annotations for visualization with any genome visualization kit such as pygenomeviz, mauve and others, it prepares the coordinates as tuples

geneprediction genome-annotation transcriptome-analysis transcriptome-annotation transcriptome-assembly transcriptome-wide trinity

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/shell-repo-generator

a shell sudo repor generator for finding and updating the packages on the cloud instances and also the slurm and the pbs instances. just provide the instance name and the package to be seached and it will bring down all the install available.

cloud cloud-computing linux-shell slurm-cluster

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/shiny-metabolic_analysis

a shiny application for the analysis of the metabolic genome and to provide the visualization and the mapping analysis. It will also allow you to make the multiple mapping terms

python3 rshiny rshinyapp shiny-applications shiny-python shiny-r

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/genome-datautilities

genome-datautilies for genome analysis and also sequence and string manipulations.

bash bash-script bashpro chpc cluster computing-cluster computing-framework programming shell shell-script

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/zenity-processid-application

a zenity based processid and it will kill automatically the process id after plotting

cluster-computing network network-programming processes zenity-gui

Last synced: 22 Feb 2025

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

A genome annotation length calculator written in ruby. It invokes the shell subprocess with in ruby to parse the iterators at the faster rate. if you have dozens of genome sequenced, simply mention the column number and the iterator will hash the length. added support for the features as

bioinformatics genome-analysis genome-annotation ruby-gem

Last synced: 22 Feb 2025

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

a R function to estimate the proportion of the pangenome across the species after the orthology runs. It makes the proportion of the table across the species. You can provide the species file and then estimated

bioinformatics pangenome rprogramming

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/plant-resistance-gene-fetcher

a custom function to fetch the dna and the protein sequence from the plant resistance gene database and get the corresponding dna_sequence and the protein_sequence.

bioinformatics disease-detection diseaseresistance plantgenomics plantresistance sequence-analysis sequence-labeling

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/odd-ratio-estimator

This function will take a data frame of the outbreak and will predict the odd ratios and the specific likelihood of occurrence of the disease in that specific geographical location

genomic-data-analysis genomics-data infectious-disease-models infectious-diseases odds-ratio python risk-analysis risk-assessment risk-management

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/neural-network-metagenomics

a function to generate the hidden layers from the given fasta and the expression files. it takes the replicate columns and then calculates the expression and length as a hidden layer. Applying to the transcriptomics, meta transcriptomics and other expression datasets

bioinformatics machinelearning machinelearningalgorithms metagenomics metatranscriptomics neural-network neural-networks

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/phytozome-pacid-fetcher

this function takes ids file with the gene of interest and the phytozome gff files and will fetch the pacid for the genes of interest.

annotation-processor bioinformatics bioinformatics-analysis genome-analysis genome-annotation phytozome

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/protein-multialign-gem

a protein miltalign gem for the sequence extractions, upstream and downstream promoters, enhancers and also the motifs localized near to the mRNA

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pangenomemetagenomicsnormalizer

a pangenome metagenomics normalizer, given a gene ontology based presence and absence and a species file, it first summarizes the count across the species and then takes the count of the gene ontologies and present a ratio The higher the ratio the more presence of that ontology across the species.

bacterial-genome-analysis bacterialmetagenomics bioinformatics fungal-metagenomics metagenomics metagenomics-counts pangenomics

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/awk-plotter

a awk based sort index way to plot the files or the directories across the dockers and intergrate this in your ~/.bashrc or the ~./zshrc or a cron job for managing the disk space across dockers

awk awk-programming-language cluster-computing containers docker filesystem watcher

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/paf-graphs-plotter

a paf formatter and plotter for the graph analysis and see the alignment of the miniasm and it uses faster approach for the analysis of the paf alignments and also outputs and extracts the corresponding paf alignments for the graphs.

alignment-algorithm alingmentplotter graph miniasm paf visualization-tools

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/maf-diagonal-information

a maf diagonal information written in AWK for getting the specific corrdinates of the alignment present on the plus or the minus strand and getting their diagonal information so that it can be used as node.

awk-programming-language bioinformatics diagonal mafalignments pacbiohifi

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/mirna-neural-network

A function to prepare the neural network sequence for the miRNA predictions. It uses the target prediction and the transcript and prepares the targets for the neural networks

bioinformatics machine-learning machine-learning-algorithms microrna-sequence microrna-target-prediction microrna-targets micrornas neural-machine-translation neural-networks

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/miniprot-ruby-gem

a ruby gem for the parsing and extraction of the miniprot alignments to extract locus specific, ids specific, and score and iters

bioinformatics genome-analysis genome-annotation ruby-gem rubyprogramming

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pbs-altair-pro-bash

This repository contains the code for the PBS Altair Pro at CHPC and you can save this code ending with .sh and run the script as .sh and you dont have to remember the PBS Pro manual.

altair bash-script bash-scripting computing-cluster high-performance high-performance-computing pbs pbs-torque

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/plant-resistance-gene-miner

plant resistance gene miner which uses a regular expression plus a web scrap approach and given a resistance gene id, it will return the genbank id

bioinformatics bioinformatics-analysis genemining plantdisease plantdiseaseclassification plantgenomics resistancegenes

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/miniprot-compleasm

a list of the awk expression that can be used for the preparation of the single and the duplicated genes across the reference genome mapping using the reference protein datasets

bioinformatics bioinformatics-tool genome-analysis genome-annotation genome-assembly genome-completion

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pacbiohifi-universitat-potsdam

a slurm configuration analytical pipline for the analysis of the pacbiohifi sequencing genomes using the verkko, hifiasm and the genomeasm4pg. only provide the link to the sequencing or the files with the folder and rest it will do the work

genome-annotation genome-assembly genome-sequencing pacbio-data pacbio-sequencing slurm-cluster slurm-job slurm-workload-manager

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/literature-bert

python class for literature training from biomedical literature. It reads the text from the pdf and then implements the tokens and then uses the BERT model to train the model

bert-embeddings bert-models bioinformatics genomics literature-mining machine-learning-algorithms natural-language-processing naturallanguageprocessing

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/lastz-alignment-awk

genome sorting and plotting the length alignment from the lastz alignment for the node calculations right before you import them for the calculations.

genome-analysis genomealignment hifi pacbio-data pacbio-sequencing

Last synced: 22 Feb 2025

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

dplyr version of visualization of all the coding regions for a specific ids from protein alignment.

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/linear-regression-bounded

fitting a linear regression on the height and the bolting time of the lettuce phenotypes to see if there can be a linear regression to be established

bioinformatics linear-models linear-regression machinelearning memorylinearregression python rprogramming

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/ontologies-semanticweb

a ontology to the relation patcher that will prepare the distance implementation. It will prepare the files for the nextworkx also.

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/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

bioinformatics fungal-genomes fungal-its fungal-metagenomics fungalgenomics metagenomics metagenomics-data

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/devops-backup-file

code for the PBS backup simulator and you can run your code with in the PBS simulator to avoid any breakage and system configurations loss

computing-cluster high-performance high-performance-computing pbs pbs-torque python3

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/expression-sequence-ml

a automated framework for the sequence to expression machine learning. it takes the fasta sequences, expression file from the expression analysis and then writes the pickle file

bioinformatics expression-language machine-learning machine-learning-algorithms sequence-labeling sklearn-classify sklearn-library

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/flux-models-ruby

implementation of mathematical models in ruby bindings and also as shards for the crystal. This repository will be updated regularly for the complete integration

bioinformatics mathematical-functions mathematical-modelling mathematical-programming ruby-gem rubylang rubylanguage rubyprogramming

Last synced: 22 Feb 2025

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

a docker server profiling configuration based on the docker or the pod ip address and it will print the latency in your terminal.

computing-cluster computing-framework docker docker-container ruby servers

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/awk-pacbiohifi

awk simulators for the pacbiohifi assembly reading from the graphs. easy to use awk for the coverage and the length files. udpating later on with the complete awk functionalities for the compilation into the direct kernels.

awk-language awk-programming-language awk-script genome-analysis genome-assembly hifi pacbio-data pacbio-sequencing

Last synced: 22 Feb 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: 22 Feb 2025

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

a github extender which will create the start and stop of the github cli actions for the repositories and will make it easier for the git clone. You dont have to follow any page, it just need the username and the number of the repositories and will make the gitclones.

github-actions github-apps github-config githubcli githubclient

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/docker-network-latency-plotter

a docker network latency plotter coded which is a part of the bundle docker swarm management and this subpart will check and plot all the docker network latency and also prune them if they are sleeping or are dead

cluster-computing docker docker-container docker-swarm dockernetwork dockernetworking

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/ena-api-access

a ENA archive access function written for accessing the archives and generating the fasta directly without using the multiple link page visits. Implementing a short route and a stored index for the same.

api-client api-wrapper apim-devops embl embl-ebi

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/docker-ruby-lister

I coded a ruby class coded to get all the information on the running docker containers with their names and sizes. You can initialize the class and then pull all the information.

cluster-computing docker docker-container docker-image swarm-cluster

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/evolutioncal

A evolutionary function in ruby which given a similarity score means the number of the similar bases and the dissimilar bases and then the sequence rate and the divergence rate calculates a ratio which can tell us how much sequencing depth to be covered

evolution evolutionary-computation evolutionary-strategy ruby rubyprogramming sequence-analysis

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/bacterial-site-checker

A faster implementation of the string search for the check of the insertion elements and the CRISPR sites if present in the genome string and then clip those insertion sites and get a clean genome.

bacterial-genomes bioinformatics fungalgenomics insertionelement sitesplicer

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/coding-stitcher-pangenome

a coding sticher for genome annotations, which stitch all your coding regions coming out of the exon alignments and will produce the gene visualization for the pangenome

annotation-tool bioinformatics bioinformatics-algorithms genome-alignment genome-annotation protein-alignment protein-sequences

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/gawk-awk-paf-alignments

a combination of the gawk and the awk basic compiler to create a function that will estimate the aligned genome fractions from the paf alignment of the genome long reads to the genome. This includes multiple functions which also allow for the filtering of the quality alignments before estimating the genome length coverage.

gawk genome-analysis genome-assembly genome-sequencing pacbio-data paf

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/bacterial-tolerance-rate-svm

a support vector based machine learning to predict the tolerance rates in the bacterial infections. It uses eps-regression and although the c-type classification can be applied if you want to predict the time variable

bioinformatics machine-learning machine-learning-algorithms support-vector-machine support-vector-machines support-vector-regression

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/cirad-meso-bioinfo

a general purpose utility to check the available modules from the cirad servers and will provide support as you dont have to load the modules and then go through the list. It directly reads the bin files from the agi_bin

cluster computing-cluster high-performance-computing server-side-rendering

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/arabidopsis-api-tair

this repository contains a function which will make your access to tair datasets easier for the arabidopsis research. Run this function and it will run and download the arabidopsis datasets and make the required analysis. It will make all the dictionary with nested lists and tuples which will provide a easy access to the tair dataframe

annotation-processing annotation-processor annotations arabidopsis arabidopsis-thaliana genome-analysis genome-assembly tair tair3

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/arabidopsis-maf-cap-accessions

arabidopsis-maf-cap-accessions. genome extraction, alignments, visualization, phylogenomics, ancestral tree

arabidopsis arabidopsis-thaliana maf phylogeny phylogeny-plots visualization

Last synced: 22 Feb 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: 22 Feb 2025

https://github.com/gauravcodepro/docker-yaml-bioinformatics

a suite of the docker yaml bioinformatics that i wrote for the working.Each of the docker yaml is specific

bioinformatics docker dockerfiles genome-analysis

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/bacterial-model-fractions

This repository contains the risk model function of the disease model in virbrio infections and how can be modeled to estimate the attributable rates

infectious-disease-models infectious-diseases modelling outbreak-analysis outbreak-data-analysis outbreak-detection python risk-analysis vibrio-cholerae

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/miniprot-protein-annotator

from protein alignments to deep learning preparatory.

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

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/protoyping-matlab-javascript

a javascript element selection prototyping for matlab machine learning.

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pacbio-hifibrowse-electron-app

a electron based Pacbio hifi browser for visualization of pacbiohifi aligned long reads.

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/visualfreq

alignment visualization and phylogeny plotting for genome aliged regions.

alignment-strategies bioinformatics genome-alignment genome-analysis r-language r-programming

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/sra-explorer

a native enumaltor for the sra explorer and it will explore the sra and will bring all the information and will generate the go to files for the analysis. You simply have to provide as many as much as posisble SRA accessions for the use of the same.

genome ncbi-sra ncbi-submission pangenome

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/pacbiohifi-meryl

plotting tools for pacbiohifi meryl hapmers and yak kmers

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/miniprot-protein-alignments

a miniprot alignments to get the alignment ranges for the protein alignments that were done to generate the hints and also to generate the tabulated table for the length preparation

bioinformatics genome-annotation gff-files gff3-format proteinalignment

Last synced: 22 Feb 2025