Sivakumar Krishnamoorthy's repositories
ImageColorAnalysis
ImageColorAnalysis is a repository with a Python script for color analysis in images using ImageMagick. It generates bash scripts for individual JPG images to analyze specific colors. It provides a flexible solution for extracting color information from images, applicable in various domains such as image classification and data analysis.
small-RNA-Seq-Analysis
scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results
miRNASeq-DE-Analysis-QC
Performing RNA-Seq data analysis and quality control using DESeq2 in R.
Perseus-MS-Proteomics-Venn
Mass spectrometry Perseus Data analysis
RBP-Data-Processing
RBP-Data-Processing is a repository containing R code for processing RNA-binding protein (RBP) datasets. The code imports the data table, performs data cleaning and transformation operations, and saves the processed dataset. It provides a convenient and reproducible workflow for analyzing RBP data obtained from external sources.
RNASeq-Analysis-JunctionSeq-QoRTs
This repository provides scripts for RNA-Seq data analysis using JunctionSeq and QoRTs, enabling quality control, differential splicing analysis, and generation of browser tracks.
bam2bai
create bai file from respective bam file
Database-links
This word document contains useful collected databases
databricks-notebooks-1
Collection of Databricks and Jupyter Notebooks
Deseq2-Annotated-Data-Processing
Filter DE genes based on log2Folchange, FDR value or both
elegans-trans-splicing
Source code repository for "Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs. Bernard, et al. 2022"
exon-bed-generator
Exon BED Generator: A script to download, process, and generate a BED file with exon coordinates for Homo sapiens from a GTF file
gene-id-retrieval-from-TAIR
Gene ID Retrieval from TAIR: R code to retrieve gene IDs from TAIR (The Arabidopsis Information Resource) and export them as CSV files
gene-info-extractor
Gene Info Extractor: A Python script to extract gene information and annotations from CSV data
GTF-Filter-for-Biologists
A Python script to filter and extract information from GTF files based on chromosome names, designed to be easily accessible for biologists without extensive programming experience.
Hints-for-statistics-and-machine-learning-models
This file will give you an overall idea to choose appropriate statistical test
PDF-File-Finder
a simple Python script that helps you find and list all PDF files in the current directory. It provides an easy way to quickly locate and work with PDF files within a given folder.
ProteinMPNN
Code for the ProteinMPNN paper
R-Markdown-Dataset-Analysis
R Markdown documentation template for two NGS datasets
rna-Seq-ScaledLengthTPM
To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Schizosaccharomyces-pombe-Chip-seq-analysis
After getting the bed file from the Peak calling, we can annotate and create all downstream analysis of two sets of data
shiny-scatter-plot-app
This repository contains a Shiny app that allows users to create interactive scatter plots by selecting the X and Y axes and customizing the point color. The app utilizes the shiny package in R to provide a user-friendly interface and the ggplot2 package for creating visually appealing plots.
sivkri
Config files for my GitHub profile.
spark-monitoring
Monitoring Azure Databricks jobs
SpliceAI
A deep learning-based tool to identify splice variants
Training-modules
Materials for short, half-day workshops