joshuagryphon / plastidView external linksLinks
Position-wise analysis of sequencing and genomics data
☆41Jul 6, 2023Updated 2 years ago
Alternatives and similar repositories for plastid
Users that are interested in plastid are comparing it to the libraries listed below
Sorting:
- Ribosome profiling analysis framework as described in de Klerk E., Fokkema I.F.A.C et al (2015). Alignment, triplet periodicity analysis,…☆12May 16, 2023Updated 2 years ago
- TFFM framework☆13Sep 22, 2025Updated 4 months ago
- Riborex: Fast and flexible identification of differential translation from Ribo-seq data☆12Apr 9, 2021Updated 4 years ago
- This is the repository accompanying the pre-print titled, "Genome-wide analyses of 200,453 individuals yield new insights into the causes…☆13Jun 9, 2022Updated 3 years ago
- A JBrowse plugin for creating sashimi or junction style plots from RNA-seq data☆14Apr 30, 2021Updated 4 years ago
- ☆57Mar 31, 2020Updated 5 years ago
- A python script used to annotate genomic intervals.☆18May 29, 2020Updated 5 years ago
- Visual exploration of large genome interaction matrices with interactive small multiples.☆13Dec 1, 2021Updated 4 years ago
- ☆13Sep 5, 2017Updated 8 years ago
- Training material for intermediate R / Bioconductor courses☆17Mar 15, 2023Updated 2 years ago
- Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)☆18Oct 12, 2025Updated 4 months ago
- Locating genetic regions that are "just right"☆17Oct 26, 2016Updated 9 years ago
- Webserver and command line tool for annotating engineered plasmids☆17Sep 25, 2024Updated last year
- Script to automate differential expression analysis using DESeq2, edgeR or limma-voom☆20Aug 22, 2018Updated 7 years ago
- GFF and GVF specification documents☆219Jun 18, 2024Updated last year
- Tools to gather evidence for structural variation via breakpoint detection.☆19Jan 21, 2026Updated 3 weeks ago
- A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.☆43Dec 14, 2015Updated 10 years ago
- Color DNA/RNA bases in terminal output☆21Aug 29, 2017Updated 8 years ago
- Repository of script tools, examples, and contributed code for using the MG-RAST API☆25Mar 22, 2021Updated 4 years ago
- RTG Core: Software for alignment and analysis of next-gen sequencing data.☆48May 27, 2025Updated 8 months ago
- A Framework to call Structural Variants from NGS based datasets☆22Jan 22, 2018Updated 8 years ago
- pythonic wrapper for htslib☆24Aug 8, 2017Updated 8 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Oct 31, 2019Updated 6 years ago
- RNA-Seq pipeline☆35Jul 22, 2015Updated 10 years ago
- splicing and feature maps for RBPs☆25Apr 19, 2022Updated 3 years ago
- 🍶 Genome assembly with short sequence reads☆25Jan 21, 2024Updated 2 years ago
- ☆70Aug 19, 2023Updated 2 years ago
- R package for subset- and name-aware array utility functions☆26Nov 28, 2025Updated 2 months ago
- Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing exp…☆71Apr 12, 2024Updated last year
- Load numpy arrays and HDF5 files from VCF (variant call format)☆31Jun 27, 2017Updated 8 years ago
- Python bindings for Bifrost's compacted colored de Bruijn Graph with a NetworkX-compatible API☆27Oct 20, 2023Updated 2 years ago
- Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline☆31Oct 9, 2017Updated 8 years ago
- Python package to plot sequence logos☆29Sep 21, 2023Updated 2 years ago
- TIDDIT - structural variant calling☆78Dec 8, 2025Updated 2 months ago
- (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER☆31Nov 21, 2018Updated 7 years ago
- GenomeTools genome analysis system.☆334Nov 10, 2025Updated 3 months ago
- Regression-based annotation of protein-coding sequences from ribosome profiling data☆32Jul 29, 2020Updated 5 years ago
- Documentation and tutorials worth sharing.☆10Dec 7, 2022Updated 3 years ago
- A method to identify structural variation from sequencing data in target regions☆32Sep 23, 2020Updated 5 years ago