Related resources¶
If you are interested in plastid, the following projects might also
be helpful for you:
Toolkits for interactive analysis of sequencing data¶
- Bioconductor
The R community’s massive toolset for computational biology
- HTSeq
A Python package designed for analysis of high-throughput sequencing data.
- metaseq
A Python package for analysis of genomics data. It is very similar in intent to
plastidin that it introduces simple, unified APIs to access genomic data of many file types. In addition, it includes nice plotting utilities for interactive analysis
Ribosome profiling¶
- ORF-RATER
Weissman lab tool to annotate potentially overlapping constellations of ORFs using ribosome profiling data, an estimate their respective amounts. See [FRJ+15].
- ribogalaxy
A web-based platform for analysis of ribosome profiling data, integrating riboseqr, galaxy, and other tools.
- riboseqr
A toolkit for analysis of ribosome profiling data, written in R. It implements many standard workflows.
Differential gene expression¶
- DESeq2
Statistical models for assessment of differential gene expression, applicable to RNA-seq, ribosome profiling, and many other types of high-throughput sequencing data
DESeq2 can be used to test for significant differences in expression counts obtained using the
csorcounts_in_regionscripts- cufflinks
A software suite for transcript assembly and differential expression analysis of RNA-seq data
- kallisto
Software for measurement of gene expression from RNA-seq data
General-purpose manipulation¶
- Samtools
Manipulate read alignments in SAM and BAM files on the command line
- Pysam
Python bindings for Samtools.
plastiduses Pysam internally for parsing of BAM and tabix-compressed files- bedtools
Fast command-line tools that perform arithmetic on annotations of continuous genomic features, and that count read coverage and/or other properties for those regions
- pybedtools
Python bindings for bedtools
- Jim Kent’s utilities
Convert text-based genomic files to randomly accessible, indexed binary formats (e.g. BED to BigBed, wiggle and bedGraph to BigWig, FASTA to 2bit, et c)
Genome browsers¶
- Integrative Genome Viewer
A lightweight and versatile genome browser created by the Broad Institute. IGV is suitable for laptops & desktops.
- UCSC Genome Browser
A web-based genome browser developed by University of California, Santa Cruz. The UCSC Genome Browser integrates with UCSC’s large database of genomes, annotations, and tracks of quantitive data. It also offers many tools for visualization and manipulation of genomics data.