sivkri/survival-analysis-end-to-end

A comprehensive end-to-end survival analysis project using classical and deep learning models with clinical data, including preprocessing, modeling, evaluation, and interpretability.

Language: Jupyter Notebook - Size: 1.1 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 1 - Forks: 0

sivkri/advanced-time-series-forecasting

A comprehensive notebook for traditional, ML, DL, and Transformer-based time series forecasting with preprocessing, evaluation, interpretability, and ensembling

Language: Jupyter Notebook - Size: 367 KB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0

sivkri/interactive-ab-testing

This repo provides an interactive A/B dashboard built with Streamlit. It allows you to simulate or use real A/B testing data, perform statistical analysis (Frequentist and Bayesian), and visualize conversion rates and other business metrics over time. It aims to help to make data-driven decisions on which model (or variant) performs best.

Language: Jupyter Notebook - Size: 151 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sivkri/GenAI-cluster-analyzer

Built to combine the power of traditional ML and GenAI for meaningful and interpretable clustering insights in biomedical, financial, and general-purpose datasets

Language: Jupyter Notebook - Size: 1.21 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sivkri/sivkri

Config files for my GitHub profile.

Size: 19.5 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sivkri/regression-ml-dl-genai-app

An interactive regression analysis platform powered by Machine Learning, Deep Learning, and Generative AI — built with Streamlit for real-time, explainable model exploration.

Language: Jupyter Notebook - Size: 3.06 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sivkri/interactive-cancer-risk-predictor-ml-dl

Designed for reproducible research, real-time insights, and easy deployment.

Language: Jupyter Notebook - Size: 65.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sivkri/RRHO2-Analysis-of-Differential-Gene-Expression

Rank-Rank Hypergeometric Overlap (RRHO2) analysis on gene expression data

Language: HTML - Size: 338 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

sivkri/NLP-LLM-TextMining_GeneSearch

Text Mining (PubMed Search) with NLP & LLM

Language: Jupyter Notebook - Size: 31.3 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

sivkri/GeneExpression-MachineLearning

Supervised Machine Learning for Gene Expression Analysis

Language: Jupyter Notebook - Size: 3.72 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

sivkri/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.

Language: Python - Size: 2.07 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0

sivkri/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

Language: Shell - Size: 1.71 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

sivkri/Perseus-MS-Proteomics-Venn

Mass spectrometry Perseus Data analysis

Language: Jupyter Notebook - Size: 330 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

sivkri/Deseq2-Annotated-Data-Processing

Filter DE genes based on log2Folchange, FDR value or both

Language: Python - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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.

Language: Python - Size: 20.5 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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

Language: R - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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.

Language: R - Size: 4.88 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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

Language: Shell - Size: 3.91 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/gene-info-extractor

Gene Info Extractor: A Python script to extract gene information and annotations from CSV data

Language: Python - Size: 52.7 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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

Language: R - Size: 116 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/bam2bai

create bai file from respective bam file

Language: Shell - Size: 2.93 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/R-Markdown-Dataset-Analysis

R Markdown documentation template for two NGS datasets

Language: HTML - Size: 3.88 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/MyWebApp

MyWebApp: A simple and lightweight web application.

Language: PHP - Size: 3.55 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

sivkri/miRNASeq-DE-Analysis-QC

Performing RNA-Seq data analysis and quality control using DESeq2 in R.

Language: R - Size: 110 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

sivkri/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.

Language: R - Size: 14.6 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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.

Language: Python - Size: 2.72 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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.

Language: R - Size: 991 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/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.

Language: R - Size: 601 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sivkri/Hints-for-statistics-and-machine-learning-models

This file will give you an overall idea to choose appropriate statistical test

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sivkri/ApacheSpark Fork of martandsingh/ApacheSpark

This repository will help you to learn about databricks concept with the help of examples. It will include all the important topics which we need in our real life experience as a data engineer. We will be using pyspark & sparksql for the development. At the end of the course we also cover few case studies.

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sivkri/Azure-Databricks Fork of tomaztk/Azure-Databricks

Azure Databricks - Advent of 2020 Blogposts

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sivkri/databricks-notebooks-1 Fork of syedhassaanahmed/databricks-notebooks

Collection of Databricks and Jupyter Notebooks

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sivkri/spark-monitoring Fork of mspnp/spark-monitoring

Monitoring Azure Databricks jobs

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sivkri/databricks-notebooks Fork of yokawasa/databricks-notebooks

Collection of Sample Databricks Spark Notebooks ( mostly for Azure Databricks )

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sivkri/OmicsPLS_ShortCourse Fork of selbouhaddani/OmicsPLS_ShortCourse

Statistical course on multi-omics data integration

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sivkri/BDA_R_demos Fork of avehtari/BDA_R_demos

Bayesian Data Analysis demos for R

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sivkri/BDA_py_demos Fork of avehtari/BDA_py_demos

Bayesian Data Analysis demos for Python

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sivkri/rna-seq-pipeline Fork of ENCODE-DCC/rna-seq-pipeline

Size: 477 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

sivkri/DataScienceResources Fork of jonathan-bower/DataScienceResources

Open Source Data Science Resources.

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sivkri/Python Fork of TheAlgorithms/Python

All Algorithms implemented in Python

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sivkri/33-js-concepts Fork of leonardomso/33-js-concepts

📜 33 JavaScript concepts every developer should know.

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sivkri/awesome-cheatsheets Fork of LeCoupa/awesome-cheatsheets

👩‍💻👨‍💻 Awesome cheatsheets for popular programming languages, frameworks and development tools. They include everything you should know in one single file.

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sivkri/Front-End-Checklist Fork of thedaviddias/Front-End-Checklist

🗂 The perfect Front-End Checklist for modern websites and meticulous developers

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sivkri/developer-roadmap Fork of kamranahmedse/developer-roadmap

Interactive roadmaps, guides and other educational content to help developers grow in their careers.

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sivkri/data-scientist-roadmap Fork of MrMimic/data-scientist-roadmap

Toturials coming with the "data science roadmap" picture.

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sivkri/You-Dont-Know-JS Fork of getify/You-Dont-Know-JS

A book series on JavaScript. @YDKJS on twitter.

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sivkri/30-seconds-of-code Fork of 30-seconds/30-seconds-of-code

Short JavaScript code snippets for all your development needs

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sivkri/python-mini-projects Fork of Python-World/python-mini-projects

A collection of simple python mini projects to enhance your python skills

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sivkri/ds-cheatsheets Fork of FavioVazquez/ds-cheatsheets

List of Data Science Cheatsheets to rule the world

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sivkri/learn-python Fork of trekhleb/learn-python

📚 Playground and cheatsheet for learning Python. Collection of Python scripts that are split by topics and contain code examples with explanations.

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sivkri/css-protips Fork of AllThingsSmitty/css-protips

⚡️ A collection of tips to help take your CSS skills pro 🦾

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sivkri/awesome-datascience Fork of academic/awesome-datascience

:memo: An awesome Data Science repository to learn and apply for real world problems.

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sivkri/learn-python3 Fork of jerry-git/learn-python3

Jupyter notebooks for teaching/learning Python 3

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sivkri/free-python-books Fork of pamoroso/free-python-books

Python books free to read online or download

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sivkri/ibm3202 Fork of pb3lab/ibm3202

Google Colab Tutorials for IBM3202

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sivkri/Data-science-best-resources Fork of tirthajyoti/Data-science-best-resources

Carefully curated resource links for data science in one place

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sivkri/Deep_learning_examples Fork of liyu95/Deep_learning_examples

Examples of using deep learning in Bioinformatics

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sivkri/pfb2019 Fork of prog4biol/pfb2019

Programming for Biology 2019

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sivkri/R-graph-gallery Fork of holtzy/R-graph-gallery

A website that displays hundreds of R charts with their code

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sivkri/RNA-Seq-Model-Organism-Arabidopsis-thaliana Fork of CBC-UCONN/RNA-Seq-Model-Organism-Arabidopsis-thaliana

RNA Seq Model Organism Arabidopsis thaliana using paired end reads

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sivkri/aradeepopsis Fork of Gregor-Mendel-Institute/aradeepopsis

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

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sivkri/bioinformatics-workbook Fork of williamrowell/bioinformatics-workbook

Bioinformatics Workbook repository

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sivkri/Database-links

This word document contains useful collected databases

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sivkri/splicing-events-calculation

Calculate five major splicing events using rMATS followed by annotation

Language: Jupyter Notebook - Size: 25.4 KB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

sivkri/NGS-RNAseq-training Fork of maurya-anand/NGS-RNAseq-training

Hands-On training 2015

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sivkri/NGS-Variant-Analysis-training-2016 Fork of maurya-anand/NGS-Variant-Analysis-training-2016

Adapted session for a one-day training

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sivkri/venn-tools Fork of maurya-anand/venn-tools

R scripts to plot Venn diagrams for 2,3,4-way Venn from counts

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sivkri/Source-Code-from-Tutorials Fork of maurya-anand/Source-Code-from-Tutorials

Here is the source code from all of my tutorials.

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sivkri/Complete-Python-3-Bootcamp Fork of maurya-anand/Complete-Python-3-Bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

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sivkri/nextflow-scif Fork of maurya-anand/nextflow-scif

This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.

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sivkri/bioinformatics-cafe Fork of maurya-anand/bioinformatics-cafe

Unsorted scripts for bioinformatics

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sivkri/awesome-pipeline Fork of maurya-anand/awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

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sivkri/AppliedGenomeResearch Fork of maurya-anand/AppliedGenomeResearch

course about NGS data processing: genomics and transcriptomics

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sivkri/APPLS Fork of bpucker/APPLS

Applied Python Programming for Life Scientists

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sivkri/IARC-nf Fork of maurya-anand/IARC-nf

List of IARC bioinformatics nextflow pipelines

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sivkri/patterns Fork of maurya-anand/patterns

A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

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sivkri/BADAS_Nextflow_Tutorial Fork of maurya-anand/BADAS_Nextflow_Tutorial

Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology

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sivkri/code Fork of maurya-anand/code

Compilation of R and Python programming codes

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sivkri/nf_ngschool20 Fork of maurya-anand/nf_ngschool20

Nextflow training material for NGSchool summer 2020

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sivkri/R_for_data_science Fork of maurya-anand/R_for_data_science

R for data science with tidyverse and ggplot2

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sivkri/Lab_Knowledge_Base Fork of maurya-anand/Lab_Knowledge_Base

A small collection of useful tutorials and links

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sivkri/datasciencecoursera Fork of maurya-anand/datasciencecoursera

Data Science Repo and blog for John Hopkins Coursera Courses. Please let me know if you have any questions.

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sivkri/shinyjs Fork of maurya-anand/shinyjs

💡 Easily improve the user experience of your Shiny apps in seconds

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sivkri/genozip Fork of maurya-anand/genozip

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Size: 165 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

sivkri/free-programming-books Fork of maurya-anand/free-programming-books

:books: Freely available programming books

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sivkri/MidbrainOrganoid_scRNAseq Fork of neuroeddu/MidbrainOrganoid_scRNAseq

R scripts for filtering, integrating, clustering, annotating and looking at gene expression within clusters from two samples of three midbrain organoids

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sivkri/rnaseq_tutorial Fork of griffithlab/rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

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sivkri/nQuire Fork of clwgg/nQuire

A statistical framework for ploidy estimation using NGS short-read data

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sivkri/smudgeplot Fork of KamilSJaron/smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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sivkri/Compacta Fork of bioCompU/Compacta

A fast contig clustering tool

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sivkri/Panoramic Fork of MayroseLab/Panoramic

A package for constructing eukaryotic pan-genomes

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sivkri/Viral-Metagenomics-2021 Fork of MGXlab/Viral-Metagenomics-2021

Size: 3.12 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

sivkri/rnaseq Fork of maurya-anand/rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

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sivkri/demo-genomics-workflows Fork of wleepang/demo-genomics-workflows

Size: 140 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

sivkri/Long-reads-Sequencing-of-SNCA-in-Diseases Fork of williamrowell/Long-reads-Sequencing-of-SNCA-in-Diseases

Scripts accompanying Tseng E, Rowell WJ, Glenn O-C, Hon T, Barrera J, Kujawa S and Chiba-Falek O (2019) The Landscape of SNCA Transcripts Across Synucleinopathies: New Insights From Long Reads Sequencing Analysis. Front. Genet. 10:584. doi: 10.3389/fgene.2019.00584

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sivkri/pyspark_linux Fork of manojmanivannan/pyspark_linux

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