RNA-seq workflow using STAR and DESeq2
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gene-expression-analysis
Here are 26 public repositories matching this topic...
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
bioinformatics next-generation-sequencing rna-seq-analysis mirna mirna-seq gene-expression-analysis mirna-sequencing small-rna-analysis
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Bioinformatics package created in C# and python, which can analyze biological data such as DNA, RNA and protein sequences, Biological Databases Scrapping, As well as 'GEO Analysis' offers a variety of analysis on RNA-seq. Preprocessing, parsing various biological file formats (FASTA, PDB, SOFT, FASTQ, etc.), this all using C# language and dotnet.
biological-data-analysis bioinformatics-tool gene-expression-analysis csharp-bioinfo biological-file-formats
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- C#
A tutorial demonstrating how to analyze gene expression data using elastic net models to predict patient responses to immunotherapy, focusing on regularization, cross-validation, and feature importance.
cross-validation precision-medicine feature-importance elastic-net-regression gene-expression-analysis
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RNA-Seq analysis pipeline for investigating transcriptional changes during mammalian cardiac regeneration.
rna-seq-pipeline differential-expression-analysis gene-expression-analysis transcriptional-profiling
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Gene expression analysis approaches using knowledge graph of Protein-Protein Interaction from STRING database
knowledge-graph statistical-analysis betweenness-centrality eigenvector-centrality bubble-plot geo-datasets ppi-networks geo-data-processing centrality-measures covid-19 gene-expression-analysis data-processing-and-analysis dice-algorithm
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My Spring 2024 term project for NYU's Applied Genomics graduate course (M.S. Biology). Using data from Brar et al, analysis of average gene expression on certain regions of baker's yeast chromosomes during traditional time course meiosis.
rna-seq gene-expression biochemistry rna-seq-analysis meiosis saccharomyces-cerevisiae yeast-dataset time-course gene-expression-analysis
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Identification of small molecule therapeutics against COVID-19 using phytochemical screening, gene expression prediction, enrichment analysis, and druglikeness evaluation.
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Identifies Multiple Peaks and Qauntifies Transcripts. Quantifies gene expression from TAGseq experiments by identifying transcript isoforms containing distinct 3' UTRs/terminal exons.
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This project aims to identify gene expression patterns associated with different conditions or diseases, leveraging advanced data processing and model training techniques. The analysis includes preprocessing RNA-Seq data, training multiple classifiers, and evaluating their performance to determine the most effective models for such biological data.
python machine-learning random-forest jupyter-notebook classification rna-seq-data gene-expression-analysis
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Docker based GUI for in-depth but accessible scRNA annotation and analysis
docker bioinformatics genomics r-shiny 10x-genomics single-cell-rna-seq single-cell-analysis gene-expression-analysis cell-clustering
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Investigation of Domains of Coordinated Expression (DCEs) using genome-wide transcriptome profiles from Systemic Lupus Erythematosus patients undergoing Belimumab/Benlysta treatment.
rna-seq-analysis genome-architecture benlysta gene-expression-analysis gene-expression-correlation domains-of-coordinated-expression systemic-lupus-erythematosus
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Gene expression analysis and classification using XGBoost and Differential Expression Analysis (DES)
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Sleeping is an essential need for animals. Many studies in the past have demonstrated health affections as consequence of sleep deficiency. In this project, RNA-seq analysis allows to compare gene expression in mice among sleep disruption and normal conditions.
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Code and analysis scripts for analyzing newly transcribed RNA in large-scale compound screen experiments
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In this module, you will take a deeper look at RNA-sequencing using single-cell approaches and miRNA sequencing, and investigate their impacts on gene regulation
bioinformatics rna-seq aws-s3 deseq2 scrna-seq high-throughput-sequencing differential-gene-expression microrna-sequence single-cell-rna-seq gene-expression-omnibus bulk-rna-seq aws-sagemaker gene-expression-analysis sequence-read-archive
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Prior knowledge-guided tree-based models
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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.
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A classification model to classify samples based on their gene expression profiles
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The repository contains scripts for Differential Methylation Analysis, Differential Gene Expression Analysis, Machine Learning validation of methylation markers.
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- Jupyter Notebook
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