Projects in Awesome Lists by bibymaths
A curated list of projects in awesome lists by bibymaths .
https://github.com/bibymaths/bio-sea-pearl
Sequence analysis and bioinformatics utilities in Python and Perl.
Last synced: 06 Apr 2026
https://github.com/bibymaths/clinical-trials-stats-r
R scripts for statistical analysis of clinical trials, focusing on non-parametric methods, permutation tests, and visualization. Includes Wilcoxon-Mann-Whitney tests, Kruskal-Wallis tests, and rank-based effect estimation to analyze treatment outcomes
behrens-fischer-problem clinical-trials non-parametric-statistics
Last synced: 20 Mar 2025
https://github.com/bibymaths/sequencealigner
A simple C++ program for performing Longest Common Subsequence (LCS), Global Alignment, and Local Alignment using dynamic programming. Reads sequences from input files and computes alignment scores based on match, mismatch, and gap penalties.
Last synced: 20 Mar 2025
https://github.com/bibymaths/grmap
A Snakemake pipeline for matching sequencing reads to a reference genome and annotating genomic features.
dna-sequences fasta pattern-matching perl regex sequence-labeling
Last synced: 14 Jul 2025
https://github.com/bibymaths/ifa-2022
Computational Algorithms & Data Science Projects
bioinformatics machine-learning modelling pattern-matching
Last synced: 05 Apr 2025
https://github.com/bibymaths/bachelor_thesis
Identification of Potent Biomarkers for Prostate Cancer Through AR, Mapk and M-TOR Signaling Pathways Mining
bachelor bioinformatics cancer pathway-analysis prostate-cancer thesis
Last synced: 23 Mar 2025
https://github.com/bibymaths/sars_genome_assembly
A complete pipeline for assembling and analyzing the SARS-CoV-2 genome from Illumina paired-end reads, featuring quality control, mapping, variant calling, consensus sequence generation, lineage annotation, and phylogenetic analysis. Designed for efficient and modular bioinformatics workflows.
genome-assembly illumina sars-cov-2 variantcalling
Last synced: 23 Mar 2025
https://github.com/bibymaths/python_snippets
A collection of Python scripts for bioinformatics data analysis, including tools for transcription counts, nucleotide composition, and protein sequence evaluation.
amino-acid-scoring bioinformatics data-analysis fasta-generation mathematical-evaluation nucleotide-analysis protein-sequence-analysis transcription-counts
Last synced: 29 Jul 2025
https://github.com/bibymaths/pynetphorest
A modern Python implementation of NetPhorest for kinase–substrate prediction and phosphorylation crosstalk analysis.
gradient-boosting-classifier kinase-activity-predictions kinome machine-learning phosphorylation post-translational-modifications
Last synced: 13 Jan 2026
https://github.com/bibymaths/poster_nscb16
Identification of Potential Lead Molecule for Schizophrenia Through Docking-Based Approach
computational-chemistry docking schizophrenia
Last synced: 04 Feb 2026
https://github.com/bibymaths/phoscrosstalk
ODE-based phosphorylation network model using PTMcode2/pynetphorest crosstalk predictions to build global/local coupling matrices. Fits phosphosite time-course data with DE optimization and reconstructs full protein–site activation dynamics.
Last synced: 10 Mar 2026
https://github.com/bibymaths/nf-illumina2lineage
A Nextflow pipeline for SARS-CoV-2 genome assembly and analysis from Illumina reads—includes QC, mapping, variant calling, consensus generation, lineage annotation, and phylogenetics.
genome-assembly illumina sars-cov-2 variantcalling
Last synced: 03 Jul 2025
https://github.com/bibymaths/perl_snippets
A collection of Perl scripts for solving bioinformatics problems and algorithmic challenges, including sequence analysis, alignment, and DNA assembly.
alignment amino-acids assembly bioinofrmatics dna-sequences edit-distance fibonacci hamming-distance lcs motif perl
Last synced: 14 Apr 2026
https://github.com/bibymaths/codonanalyzer
A collection of Perl scripts for analyzing DNA and protein sequences, featuring tools for rare codon detection, GC content profiling, and hydropathy plotting, optimized for Escherichia coli datasets.
codon-usage dna-sequences perl protein
Last synced: 18 Oct 2025
https://github.com/bibymaths/phoskintime
An optimization driven ODE-based modeling pipeline for analyzing cell-signaling dynamics over time.
kinase-activity-predictions kinase-modeling mrna-degradation network-analysis ode-model optimization optimization-methods
Last synced: 28 Feb 2026