analysis code repositories at Github following the link: Git

Research Students GitHub Projects: Student-GitHub-Projects

Important & Interesting project mentions:

Android utility app: This project was focused on development of android application with several use case utilities ####https://github.com/spawar2/Android-Utility-App-#### [Java: android.content.Context, android.support.test.InstrumentationRegistry, android.support.test.runner.AndroidJUnit4, org.junit.Test, org.junit.runner.RunWith]
A PHP, MySQL based online shopping portal: This project was focused on development of online shopping portal similar to Amazon and ebay Demo ####https://github.com/spawar2/Final_Project_PHP_SQL####[PHP, CSS, HTML, JavaScript: mysql_import.sql]
Machine learning for selection and classification of HIV PR resistance: [*2018:1] [**2018:9, 10,11]This project was focused on applying neural network architecture on HIV deep sequencing data Paper #### [MATHLAB, R, Python: numpy, sklearn.model, pylab, sklearn.decomposition] https://github.com/spawar2/HIV_Machine_Learning_Techniques#### PUBLICATION: Analysis of drug resistance in HIV protease Poster Link Poster Link
Java-platform-to-create-logic-circuit to evaluate-bolean-expression: This project was focused on developing a java platform to evaluate bolean expressions from computer architecture ####https://github.com/spawar2/Computer-Architecture–Java-platform-to-create-logic-circuit–evaluate-bolean-expression####
Java_SQL_MiceExperiment_Record_Tracking_Software: This project was focused on development of a java gui with record tracking features Demo ####https://github.com/spawar2/Java_SQL_MiceExperiment_Record_Tracking_Software
#### [Java: javax.swing.JFrame, javax.swing.JOptionPane, javax.swing.table.DefaultTableModel, javax.swing.table.TableModel, java.sql., javax.swing., net.proteanit.sql.DbUtils, java.sql.Connection, java.sql.Statement, java.sql.SQLException, java.util.ArrayList] PUBLICATION: RodentSQL: a software suite for colony management of animal protocols
A PHP, MySQL based electronic record keeping cloud system: This project was focused on developing electronic record keeping cloud system Demo ####https://github.com/spawar2/Electronic-Cloud-Notebook–PHP–MySQL–Apache#### PUBLICATION: Online electronic laboratory notebook: A secured cloud storage system scripted in Hypertext Pre-processor (PHP) programming language
Glycan-to-DNA-Mapping-Web-Server: This project was focused on developing a python based web platform to handle Glycan-to-DNA-Mapping quiries Demo [Python] ####https://github.com/spawar2/Glycan-to-DNA-Mapping-Web-Server#### PUBLICATION: DNA Encoded Glycan Libraries as a next-generation tool for the study of glycan-protein interactions
Patient flow simulation in EMS department: This project was focused on developing a devs-java based EMS simulation to address ED over crowding Demo [Java: DEVSJAVALab, simView., java.awt., java.io., genDevs.modeling., genDevs.simulation., GenCol.]####https://github.com/spawar2/Devs_Java_Patient_Flow_SimulationinEMS#### PUBLICATION: Developing a DEVS-JAVA Model to Simulate and Pre-test Changes to Emergency Care Delivery in a Safe and Efficient Manner
Head-Neck-Cancer–ROC–SVM–KM–Expression-Analysis: This project was focused on support vector machine analysis of HNC patients ####https://github.com/spawar2/Head-Neck-Cancer–ROC–SVM–KM–Expression-Analysis#### PUBLICATION: A Six-Gene-Based Prognostic Model Predicts Survival in Head and Neck Squamous Cell Carcinoma Patients
Interleukin_Pathway_Survival_Gene_Expression_Analysis: [*2019:10] [**2019: 8]This project was focused on gene expression analysis of Interleukin_Pathway genes [R: Biobase, GEOquery, survminer, survival] ####https://github.com/spawar2/Interleukin_Pathway_Survival_Gene_Expression_Analysis#### PUBLICATION: Predicting the prognosis for cancer patients with interleukins gene expression level Poster Link
Face-Recognition-Python: This project was focused on utilizing open CV python for facial recognition [Python: cv2, sys] ####https://github.com/spawar2/Face-Recognition-Python####
Forcasting-pipelines: This project was focused on developing 3 Forcasting-pipelines with time series data [R: ForeCA] ####https://github.com/spawar2/Forcasting-pipelines#### PUBLICATION: Techniques of Time Series Modeling in Complex Systems
Random-Forest-for-Ovarian-Breast-Cancer-Patients: [**2023: 1]This project was focused on developing a biomarker utilizing random forest technique [R: GEOquery, Biobase, preprocessCore, multiClust] ####https://github.com/spawar2/Random-Forest-on-Ovarian-Breast-Cancer-Patients#### Poster Link
GeneSearch: This project was focused on developing a java gui to search genes from public repositories Java ####https://github.com/spawar2/GeneSearch####
Clustering_Analysis_Cancer_Techniques [*2020:5] [**2020:6]: This project was focused on developing a biomarker tool utilizing clustering techniques [R: GEOquery, Biobase, preprocessCore, multiClust, ctc, gplots, dendextend, graphics, grDevices, amap] ####https://github.com/spawar2/Clustering_Analysis_Cancer#### PUBLICATION: Clustering Reveals Common Check-Point and Growth Factor Receptor Genes Expressed in Six Different Cancer Types Poster Link
Electric scooter for overcoming transportation and pollution problems: [*2021:4] ####https://devpost.com/software/ebird####. Prototype selected for Collegiate Cup Competition and TYE University Competition Qualifying Round 2019 and Entrepreneurship and Innovation Institute (ENI) Mentor Program PUBLICATION: Sustainable Intelligent Systems Poster Link
Random_Forest_Classfication_Renal_Cell_Carcinoma: This project was focused on developing a biomarker tool utilizing random forest [R: forcats, randomForest] ####https://github.com/spawar2/Random_Forest_Renal_Cell_Carcinoma#### PUBLICATION: Machine learning for identification and characterization of molecular gene signatures in progression of benign tumors
COVID19-Temperature-Dashboard: This project was focused on understanding relationship between COVID19-Temperature Paper Demo [R:shiny, highcharter, dplyr, UI, Server] ####https://github.com/spawar2/COVID19-Temperature-Dashboard####https://yalegenomics.shinyapps.io/deployment/?_ga=2.91441946.1803750112.1677552931-1693957918.1677552931
Regression-Analysis-Alzheimers-Disease: This project was focused on utilizing machine learning tools for feature classification in Alzheimers [R: MASS, car, glm.predict] ####https://github.com/spawar2/Regression-Alzheimers-Disease####
Image augmentations: [Python: keras.datasets, mnist, models, layers, tensorflow, Sequential, Dense, Conv2D, Dropout, Flatten, MaxPooling2D] #####https://github.com/spawar2/NLP-Challenge#####
Machine Learning Classification Pulmonary-Embolism-Master: This project was focused on utilizing machine learning tools for feature classification in Embolism [Python: numpy, sklearn, pandas, os, MATPLOTLIB] ####https://github.com/spawar2/Pulmonary-Embolism-Master####
DARTO: Program to identify orthologs for genes: [Python: os, Bio.Blast, ssl, tkinter, askopenfilename, filedialog] ####https://github.com/spawar2/DARTO####
Neural-Networks-for-Ovarian-Carcinomas: [*2023:1] [**26] This project was focused on utilizing machine learning tools for feature classification in Ovarian-Carcinomas: [R: curatedOvarianData, tidyverse, boot, plyr, e1071] ####https://github.com/spawar2/Neural-Networks-for-Ovarian-Carcinomas#### PUBLICATION: Common cancer biomarkers of breast and ovarian types identified through artificial intelligence
Chest-X-ray-Neural-Nets: This project was focused on utilizing CNN’s for X-ray image classification: https://github.com/spawar2/Chest-X-ray-Neural-Nets [*2023:4, 9; 2021: 17, 23] [**23, 29, 30, 37, 42] Demo Poster Link [https://github.com/rushikeshchopaderc https://in.linkedin.com/in/rushikesh-chopade-88470615b https://github.com/SurajK7/ https://in.linkedin.com/in/surajkumar1004 This project in collaboration with Rushikesh Chopade, Suraj Kumar Undergraduate student: Indian Institute of Technology (IIT), Kharagpur, India. Project: CHEST-AI: AI tool for detection of lung diseases from chest X- ray data (Spring 2021). Poster Paper Paper Paper Paper Paper https://link.springer.com/chapter/10.1007/978-981-19-9819-5_49 https://link.springer.com/chapter/10.1007/978-981-19-7660-5_7 https://www.researchsquare.com/article/rs-1129014/latest.pdf https://www.biorxiv.org/content/10.1101/2021.09.21.461307v1.abstract https://dl.acm.org/doi/abs/10.1145/3469213.3469214 http://20.169.253.49:5001/login https://aws.amazon.com/marketplace/seller-profile?id=seller-b6otd3wry7lkk https://bpb-us-w2.wpmucdn.com/campuspress.yale.edu/dist/7/3679/files/2023/10/ChestAi-300×167.png] (National Science Foundation South Carolina Established Program for Stem Cooperative Research (SC EPSCoR) RII Track-1 award funded project) [Python: fastai.vision, torchvision.models, pandas, Path]
BASELINe-Data: This project was focused on utilizing Bayesian estimation techniques for B and T cell profiling: Demo https://github.com/spawar2/BASELINe-Data######## [R Shiny: Tidyverse, UI, Server] https://yalegenomics.shinyapps.io/myapp/?_ga=2.91441946.1803750112.1677552931-1693957918.1677552931
Single-Cell-RNA-Analysis: This project was focused on single cell analysis techniques: https://github.com/spawar2/Single-Cell-RNA-Analysis & https://github.com/spawar2/Single-Cell-Analysis [Python: pandas, numpy, matplotlib.pyplot, string, anndata, defaultdict, OrderedDict, sklearn.preprocessing, TruncatedSVD]
COVID-SwabSeq-Testing-Run: This project was focused on testing Swab-Seq technique on COVID swab tests: https://github.com/spawar2/COVID-SwabSeq-Testing-Run [R: ggbeeswarm, MASS, speedglm, furrr, readxl, magrittr, tidyverse]
Object-Recognition-Python: This project was focused on object recognition using OpenCV: https://github.com/spawar2/Object-Recognition-Python [Python: numpy, os, urllib, sys, tarfile, tensorflow, zipfile, cv2, csv, time, collections, defaultdict, StringIO, matplotlib, PIL] Paper Demo
Quasi-quantum model for potentization: This project was focused on potentization analysis: https://github.com/spawar2/Shrodinger-Equation [R] Git PPT
System-Level-Programming: https://github.com/spawar2/System-Level-Programming
Data-Structures: https://github.com/spawar2/Data-Structures
CS-Introduction: https://github.com/spawar2/CS-Introduction
Advanced-Graphic-Algorithms: https://github.com/spawar2/Advanced-Graphic-Algorithms
Fundamentals of Bioinformatics: https://github.com/spawar2/Bioinformatics-scripts
CellLine Dependency Analysis: https://github.com/spawar2/CellLine-Dependency
Anovos feature engineering process to increase efficiency tool contributor: https://github.com/spawar2/Anovos-Contributor-User
Gene set enrichment analysis for RNA expression data: https://github.com/spawar2/Fold-Change-Comparisons [R: GenomicFeatures, clusterProfiler, enrichplot, ggplot2]
Kivy app interface development in R: https://github.com/spawar2/Kivy-GUI-R [Python: kivy.app, kivy.lang, Builder, Screen, ObjectProperty, Popup, Label, DataBase]
Structural-variant-Detection tool: https://github.com/spawar2/Structural-variant-Detection [R]
Program to Count-relative-frequency-of-amino-acids: https://github.com/spawar2/Count-relative-frequency-of-amino-acids [Python: itertools, product, combinations, Counter]
Text to voice conversion application: https://github.com/spawar2/Text-to-Voice-Application [Python: os, numpy, shlex, subprocess, sys, wave, deepspeech, Model, printVersions, timeit]
CT brain hemorrhage training: https://github.com/spawar2/CNN_Training [Python: matplotlib.pyplot, torch, time, numpy, collections, OrderedDict, torch.autograd, PIL, lr_scheduler, copy, json, os]
Evaluating performance of regression and classification models with prognostic markers in lung carcinomas: https://github.com/spawar2/Regression-Lung-Carcinoma [R: randomForest, caret] Paper

Hemorhage-Detection-CT-Scan: Poster [**33] https://github.com/spawar2/Hemorhage-Detection-CT-Scan [https://github.com/CoolSubash https://np.linkedin.com/in/subash-neupane-aa07ba228?trk=public_profile_browsemap This project in collaboration with Subash Neupane, [Python: numpy, pandas, pydicom, matplotlib.pyplot, math, cv2, tensorflow, keras] (Claflin University Seed award funded project) Undergraduate student: Claflin University, South Carolina, USA. (Fall 2023). Utilization of Machine Learning Techniques for Aiding Detection of Ischemic Stroke Lesion, Infarct Volumes, and Small-artery Occlusion https://www.claflin-computation.com/_files/ugd/81dd80_e12daf8e87c348c5a9347af693993739.pdf]
Techniques of brain segmentation from CT scan: https://github.com/spawar2/Image_Segmentation [Python: pydicom, numpy, cv2, os, math, pylab, matplotlib, scipy, ndimage, skimage, morphology]
Stroke risk stratification with neural nets: [**2023:36] [R: neuralnet] https://github.com/spawar2/Neural-Networks-Stroke [*2024:9][**2024:36] Paper
Nano-particles property prediction with random forests: [R Shiny: MissForest, randomForest, caret, UI, Server] Demo https://github.com/spawar2/RF-ENP#####https://yalegenomics.shinyapps.io/appenp/?_ga=2.91441946.1803750112.1677552931-1693957918.1677552931
Blood cancer expression analysis: https://github.com/spawar2/Blood-Cancer-Analysis [This project was in collaboration with Ms. A Agrawal, University of Connecticut, Special Program in Medicine (BS/MD), Experiential Learning Program Project: Identifying biomarkers between lymphoma and leukemia cancer patients (Fall 2021). CT STEM and Norwalk Science Fair (Poster)] [R: Affy, Limma]
Claflin University SMART-HOME: https://github.com/spawar2/SMART-HOME-CLAFLIN [**39] Poster Poster

Poster Poster https://github.com/Claflin-SMART-HOME [R: shiny, DT]######https://yalegenomics.shinyapps.io/app-smart-home/

[https://github.com/eniolla https://www.linkedin.com/in/priscilla-fatokun-35007119a https://github.com/mayor90/thesis https://campuspress.yale.edu/shrikantpawar/files/2023/12/SCICU-research-poster.pptx This project in collaboration with Mr. Owalabi Oluwamayowa (South Carolina Independent Colleges & Universities SCICU award funded project), Priscilla E. Fatokun (South Carolina Independent Colleges & Universities SCICU award funded project), Undergraduate student: Claflin University, South Carolina, USA. (Fall 2023). Project: SMART-HOME proposal “collection and processing of health-care data for African-American subjects from wrist wearable devices. https://campuspress.yale.edu/shrikantpawar/files/2023/12/SCICU-research-poster.pptx https://campuspress.yale.edu/shrikantpawar/files/2024/02/Priscilla-Research-Presentation-0b920a0c624e2982.pptx]
ChatGPT Testing: [Python: os, time, datetime, openai] https://github.com/spawar2/ChatGPT-Testing [https://github.com/bpritish https://www.linkedin.com/in/pritishbhave This project in collaboration with P Bhave, Senior Software Engineer, Walmart. Analyze ChatGPT’s codex to determine it’s viability to identify basic issues with provided Python code using OpenAI’s code model, current `code-cushman-001`]
Prostrate-Cancer-Biomarker-Analysis: https://github.com/spawar2/Prostrate-Cancer-Biomarker-Analysis https://www.linkedin.com/in/zion-ratchford-07514b1b9 This project in collaboration with Zion Ratchford, Undergraduate student: Claflin University, South Carolina, USA. (Fall 2023). https://campuspress.yale.edu/shrikantpawar/files/2024/04/Zion-Presentation-80fd6d81d5b4f75b-rotated-e1712021318501-225x300.jp, https://campuspress.yale.edu/shrikantpawar/files/2024/01/Final-Prospectus-Edited-7e17c09b3e8c4813.pdf, https://campuspress.yale.edu/shrikantpawar/files/2024/04/ROLE-CIRCULATION-BIOMARKERS-IN-PROSTATE-CANCER-DIAGNOSIS-4dbb44b57f793d6a.pptx [R: edgeR, hgu133plus2.db, tidyverse, Affy]
Linkedimm: Paper https://github.com/spawar2/Linkedimm [Python: plotly, tidyverse, htmlwidgets, plotly, tidyverse, htmlwidgets]
Institutional Development Award (IDeA) Networks of Biomedical Research Excellence (INBRE) Research Education of Teachers National Science Foundation South Carolina Established Program for Stem Cooperative Research (SC EPSCoR)-RET: Machine learning applications for studying check-point genes expressed in ten different human cancer types. https://github.com/spawar2/NSF-INBRE-EPSCoR-RET [ https://github.com/ethaharikanaidu This project in collaboration with Harika Baidu, teacher at Bamberg Ehrhardt High School (Summer 2022). Machine learning applications for studying check-point genes expressed in ten different human cancer types. Machine learning applications for studying check-point genes expressed in human Ovarian cancers. https://www.claflin-computation.com/_files/ugd/81dd80_1ad94ed63c6a49c887177419bdb46567.docx?dn=Etha%20project%20report.docx] [R: edgeR, hgu133plus2.db, tidyverse]
TF–IDF-term frequency–inverse document frequency: [Python] https://github.com/spawar2/term-frequency-inverse-document-frequency
National Science Foundation SCICU: Natural Language Processing (NLP) for optimizing career advancement prospects: https://github.com/spawar2/NSF-SCICU-2022. (South Carolina Independent Colleges & Universities SCICU award funded project) App Deploy: https://joshuakiplimo-resparse-resumematch-6a8pxp.streamlit.app/ Poster Link
Single-Cell-MA-plots-Crustacean-Species: Paper [R: Deseq2, ggplots] https://github.com/spawar2/Single-Cell-MA-plots-Crustacean-Species
miRNA-analysis: Paper https://github.com/spawar2/miRNA-analysis [R: DESeq2, tidyverse]
Internship: https://github.com/spawar2/INTERNSHIP [2024:**41] [This project in collaboration with Yash Singh, Sai and Mohit, Georgia Tech. Biomarker discovery in prostrate, lung and breast cancers (Spring 2024). https://github.com/yashsingh43 https://github.com/AbhayR43 https://github.com/Msai32005 https://github.com/rrchada https://github.com/arnavmadderla] [R: Tidyverse, ggplots] Poster Link
Traffic-Counter-ML: [Python: os, numpy, cv2, mrcnn.config, mrcnn.model, MaskRCNN, pathlib, twilio.rest, Client, kivy, App, Label, GridLayout, TextInput, Widget, BoxLayout, random] https://github.com/spawar2/Traffic-Counter-ML
Calcium-Interactomes: [R: CytoHubba, Cytoscape, String, GSEA] Paper https://github.com/spawar2/Calcium-Interactomes
Harr-Fisc-Transformations-Microarray [R] : [*2013:4] [**16, 17, 18] Paper https://github.com/spawar2/Harr-Fisc-Transformations-Microarray
2nd CMI-PB Prediction challenge: https://github.com/spawar2/2nd-CMI-PB-Prediction-challenge/tree/main
Binary-Search-Tree-In-Java-Implementation [Java]: https://github.com/spawar2/Binary-Search-Tree-In-Java-Implementation
HSET-Ovarian-Cancer-Biomarker: Paper [R: BGmix] [*2017:1, 2016:1] [**12] https://github.com/spawar2/HSET-Ovarian-Cancer-Biomarker
Comparative-analysis-endemic-Coronaviruses: [R: ggplots] Paper https://github.com/spawar2/Comparative-analysis-endemic-Coronaviruses
National Longitudinal Study of Adolescent to Adult Health analysis shows correlations between fast food consumption with physical and mental health of adults facing food insecurities This project was in collaboration with Mr. Madhu Gottti, Undergraduate student, Stanford University, California. Amity Public School, Connecticut, USA. Experiential Learning Program Project: Identifying biomarkers between lymphoma and leukemia cancer patients (Fall 2021). Los Osos High School, California. https://github.com/spawar2/National-Longitudinal-Study [R: Tidyverse, ggplots] Github
Acid Ceramidase in colon cancer, with Dr. Harikumar, RGCB [R: Deseq2, ggplots] Github
Speech to text conversion using BytesIO: [Python: BytesIO, b64decode, google.colab, IPython.display] https://github.com/spawar2/Speech2Text
Diabetic Retinopathy Detection [Python: tensorflow, keras, layers, numpy, pandas, random, os, shutil, matplotlib.pyplot, imread, keras.preprocessing.image, ImageDataGenerator, categorical_accuracy, sklearn.model]: https://github.com/spawar2/Diabetic-Retinopathy-Neural-Networks/tree/main
Atrial Fibrillation Detection [Python: numpy, pandas, seaborn, matplotlib.pyplot, sklearn.metrics, classification_report, sklearn.model_selection, f1_score, confusion_matrix, to_categorical, class_weight, OS, warnings]: https://github.com/spawar2/Atrial-Fibrillation-Neural-Networks
Murmur-Neural-Network: [Python: warnings, matplotlib, pylab inline, tensorflow, Keras, os, pandas, librosa, glob, matplotlib.pyplot] https://github.com/spawar2/Murmur-Neural-Network
Artificial Intelligence Based Framework for Predicting the Spread of Climate Change Related Infectious Diseases: (Scired: Scientific Research & Development) https://github.com/spawar2/SCIRED-Analysis
Neural networks on CTA in peripheral arterial diseases (PAD) [Python: pytorch, tensorflow]: https://github.com/spawar2/CTA-PAD-Neural-Nets (National Science Foundation South Carolina Established Program for Stem Cooperative Research (SC EPSCoR) RII Track-1 award funded project): https://scepscor.org/adapt-in-sc-thrust-2/. This project in collaboration with https://github.com/Caliese Caliese J. Beckford, https://www.linkedin.com/in/caliese-beckford-25851821b/?originalSubdomain=jm (Graduate student), Undergraduate student: Mr. Sabb, Dinari, (National Science Foundation South Carolina Established Program for Stem Cooperative Research (SC EPSCoR) RII Track-1 award funded project), Undergraduate student: Claflin University, South Carolina, USA. (Fall 2023). Machine learning application for biomedical device development. https://www.linkedin.com/in/dinari-sabb-0b62b51ba https://github.com/DinariSabb
Generative AI ChatBot using gpt-3.5-turbo engine [Python, HTML: numpy, pandas, pydicom, matplotlib.pyplot, math, cv2, tensorflow, keras, OPENAI, model: gpt-4-turbo]: https://github.com/spawar2/Generative-AI-ChatBot-using-gpt-3.5-turbo-engine
Summer-Undergraduate-Research-Internship-2024: [R: edgeR, hgu133plus2.db, tidyverse, Affy] https://github.com/spawar2/Summer-Undergraduate-Research-Internship-2024/tree/main This project in collaboration with Felicia Forrester: https://www.linkedin.com/in/feliciaforrester, Subash Neupane, https://github.com/CoolSubash https://np.linkedin.com/in/subash-neupane-aa07ba228?trk=public_profile_browsemap, Amrinder Singh https://www.linkedin.com/in/amrinder-singh-b74426251, Undergraduate student: Claflin University, South Carolina, USA. (Fall 2023). Machine Learning applications in computer aided diagnosis (CAD).