|
Programming
|
|
| Learn Python |
Introduction to Python with interactive examples |
| Python for Data Science | Learn applications of Python for data science |
| Python for Data Science Certificate | Earn a free code academy certificate in Python for data science |
| Learn R | Tutorials on R with interactive examples from Code Academy |
| Bash and Shell Tutorial | Bash command line basics with interactive examples |
| Command Line Basic | Tutorial on command line basics from Code Academy |
| Foundations of Coding | The basics of programming and coding from the Odin Project |
| Gladstone Bioinformatics Workshops | Workshops covering methods such as RNA-seq, pathway analysis, and whole genome sequencing |
| Machine Learning Workshop | Google's open resource machine learning lessons and resources |
|
Bioinformatics |
|
| HDOCK | Protein-protein and protein-DNA/RNA docking |
| OpenCell | Proteome-scale measurements of human protein localization and interactions |
| BioGRID | Biomedical interaction repository |
| STRING | Protein Interaction Networks & functional Enrichment Analysis |
| PRIDE | Proteomics identification database |
| The Human Protein Atlas | Open access repository of human genes & proteins |
| AlphaFold | Protein structure database |
| UniProt | Protein sequence and function repository |
| The Lasseigne Lab | Dr. Lasseigne's lab website contains resources for data analysis for brain sciences. |
| Dropviz.org | Single-cell transcriptomic data from mouse animal models |
| Enrichr | Promoter analyses and gene ontology for differentially expressed genes |
| Jaspar | Transcription factor binding sites |
| Cell Profiler | Cell image analysis software |
| KEGG Pathway Database | Pathways for molecular interactions in metabolism, genetics, and more |
| WikiPathways | Open platform database for biological pathways |
| Reactome | Visualization, interpretation, and analysis of genomic and system biology data |
| GTEx | Tissue-specific gene expression and regulation database |
| UCSC Genome Browser | Interactively visualize genomic data |
| miRMaster | comprehensive analysis framework for sncRNA-seq data |
| CAP-MIRSEQ | A comprehensive analysis pipeline for deep microRNA sequencing |
| Cell Ranger | Analysis pipelines for single-cell data |
| SEURAT | R toolkit for single-cell genomics |
| SCANPY | Python single-cell analysis pipelines |
| Monocle 3 | Analysis toolkit for single-cell RNA-seq |
| Velocyto | Estimating RNA expression dynamics in single-cell RNA sequencing data |
| Signac | R package for analysis of single-cell chromatin data |
| Burrows-Wheeler Aligner | RNA-seq alignment software |
| Bowtie 2 | RNA-seq alignment software |
| minimap 2 | Pairwise aligner for genomic and spliced nucleotide sequences |
| TopHat | A spliced read mapper for RNA-seq |
| Salmon | Tool for quantifying expression of RNA transcripts in RNA-seq data |
| Babraham Bioinformatics | Map bisulfite-treated sequencing reads to a genome of interest and performs methylation calls |
| methylKit | R package for DNA methylation analysis |
| BSMAP for Methylation | Short read mapping program for bisulfite sequencing in DNA methylation |
| Bioconductor | Analyze, manage, and store bisulfite sequencing data |
| STAR | RNA-seq aligner |
|
Statistics, Rigor, & Reproducibility |
|
| NIH Grants & Funding | NIH resources for publishing research, writing grant applications, and policies |
| NINDS Preparing Your Research Plan | NIH resources for rigorous study design and transparent reporting |
| SAMPL Guidelines | Basic Statistica Reporting for Biomedical Writing: Statistical Analyses and Methods in the Published Literature (SAMPL) |
| ARRIVE Guidelines | Author checklist of minimum items to include in a manuscript |
| STAR Methods | CellPress Methods Guide for Authors |
| PLOS Submission Guideline | Resources from PLOS One: Writing Center, Submission System, Getting started Guide, and Guideline for revisions |
| How to Report Statistics | PLOS resource on how to ensure appropriateness and rigor, avoid flexibility, and ethical result presentation |
| Center for Open Science | TOP guidelines created by journals, funding sources, and societies with ideal practices for transparent research |
| Zenodo | Distribution of big data management tools with digital library capabilities from CERN |
|
F-Series Grant Writing |
|
| Official NIH NRSA Guidelines (F31) | Official guidelines for preparing an F31 submission |
| NIH Application Guide | NIH Central Resource for Grants and Funding Information |
| Grants.gov | Search for previously or currently funded NIH projects |
| Tips on Writing NRSA Proposals | Advice from NRSA Reviewers on how to write a fundable proposal from |
| How to write a strong NRSA grant | A primer on F31 process and crowdsourced tips from UCLA |
| UAB F-series Samples | Samples of F-series grants submitted and funded from UAB students & faculty |
| F-series Check List | A guide for crafting and writing an NIH NRSA F-series training grants (F30, F31, F32) |
| Find your Officer or Specialist | UAB Search tool for identifying the appropriate program officer or specialist for your funding agency and specialty |
| Formatting Guidelines for NIH Proposals | Format for NIH proposal attachments (e.g. citations, fonts, images, etc) |
|
If you have information on additional resources email marycooper@uab.edu
|
|