.. File format links

.. _Wiggle: http://genome.ucsc.edu/goldenpath/help/wiggle.html
.. _bedGraph: http://genome.ucsc.edu/goldenpath/help/bedgraph.html
.. _SAM: http://samtools.github.io/hts-specs/ 
.. _BAM: http://samtools.github.io/hts-specs/
.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
.. _BigBed: http://genome.ucsc.edu/goldenPath/help/bigBed.html
.. _BigWig: http://genome.ucsc.edu/goldenPath/help/bigWig.html
.. _GTF2: http://mblab.wustl.edu/GTF22.html
.. _GFF3: http://www.sequenceontology.org/gff3.shtml
.. _PSL: http://genome.ucsc.edu/FAQ/FAQformat.html#format2
.. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
.. _autoSql: http://genomewiki.ucsc.edu/index.php/AutoSql
.. _UCSC file format FAQ: http://genome.ucsc.edu/FAQ/FAQformat.html
.. _reStructuredText: http://docutils.sourceforge.net/rst.html
.. _fasta: https://en.wikipedia.org/wiki/FASTA_format
.. _twobit: http://genome.ucsc.edu/FAQ/FAQformat.html#format7

.. Python links

.. _Python: https://www.python.org/
.. _Pip: https://pypi.python.org/pypi/pip
.. _PyPi: https://pypi.python.org
.. _NumPy: http://docs.scipy.org/doc/numpy/reference/
.. _SciPy: http://docs.scipy.org/doc/scipy/reference/
.. _Pandas: http://pandas.pydata.org/
.. _Pysam: http://pysam.readthedocs.io/en/latest/
.. _matplotlib: http://matplotlib.org/
.. _Biopython: http://biopython.org/wiki/Biopython
.. _Virtualenv: https://virtualenv.pypa.io/en/latest/
.. _nose: https://nose.readthedocs.io/en/latest/
.. _Sphinx: http://sphinx-doc.org/
.. _numpydoc: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
.. _twobitreader: https://pythonhosted.org/twobitreader/
.. _SeqRecord: http://biopython.org/wiki/SeqRecord
.. _Seq: http://biopython.org/wiki/Seq
.. _TwoBitFile: https://pythonhosted.org/twobitreader/twobitreader.html#twobitreader.TwoBitFile
.. _Metaseq: https://pythonhosted.org/metaseq/
.. _pybedtools: https://pythonhosted.org/pybedtools
.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html 
.. _conda: http://conda.pydata.org
.. _Anaconda: http://docs.continuum.io/anaconda/index
.. _Cython: http://cython.org
.. _ORF-RATER: http://github.com/alexfields/ORF-RATER


.. Genome browsers & data sources

.. _IGV: https://www.broadinstitute.org/igv/
.. _UCSC genome browser: https://genome.ucsc.edu
.. _galaxy: https://galaxyproject.org/


.. Organism databases
.. _UCSC: https://genome.ucsc.edu
.. _Ensembl: http://www.ensembl.org
.. _RefSeq: http://www.ncbi.nlm.nih.gov/refseq/ 
.. _SGD: http://www.yeastgenome.org
.. _Flybase: http://flybase.org
.. _Wormbase: http://www.wormbase.org
.. _ENCODE: https://www.encodeproject.org/
.. _GENCODE: www.gencodegenes.org 
.. _modENCODE: http://www.modencode.org
.. _GenBank: http://www.ncbi.nlm.nih.gov/genbank/
.. _NCBI Assembly: https://www.ncbi.nlm.nih.gov/assembly
.. _JGI: http://jgi.doe.gov
.. _Joint Genome Institute: http://jgi.doe.gov
.. _GEO: https://www.ncbi.nlm.nih.gov/geo/
.. _APPRIS: http://appris.bioinfo.cnio.es/#/

.. Non-Python software links

.. _Sequence Ontology Project: http://www.sequenceontology.org/
.. _SAMtools: http://www.htslib.org/
.. _htslib: http://www.htslib.org
.. _bgzf: http://www.htslib.org/doc/tabix.html
.. _tabix: http://samtools.github.io/hts-specs/
.. _bedtools: http://bedtools.readthedocs.io/
.. _Jim Kent's utilities: https://github.com/ENCODE-DCC/kentUtils/tree/master/src/product/scripts
.. _Tophat: http://tophat.cbcb.umd.edu/
.. _Bowtie: http://bowtie-bio.sourceforge.net/manual.shtml
.. _Bowtie 2: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
.. _cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
.. _BWA: http://bio-bwa.sourceforge.net
.. _STAR: https://github.com/alexdobin/STAR
.. _blat: http://genome.cshlp.org/content/12/4/656.full
.. _Cigar: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _DESeq: http://www-huber.embl.de/users/anders/DESeq/
.. _DESeq2: http://bioconductor.org/packages/release/bioc/html/DESeq2.html
.. _kallisto: http://pachterlab.github.io/kallisto/
.. _Bioconductor: http://www.bioconductor.org/
.. _R: http://www.r-project.org
.. _fastx toolkit: http://hannonlab.cshl.edu/fastx_toolkit/
.. _riboseqr: http://bioconductor.org/packages/release/bioc/html/riboSeqR.html
.. _ribogalaxy: http://ribogalaxy.ucc.ie
.. _Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
.. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

.. Our links

.. _plastid_repo: https://github.com/joshuagryphon/plastid
.. _plastid_issues: https://github.com/joshuagryphon/plastid/issues
.. _our issue tracker: https://github.com/joshuagryphon/plastid/issues 
.. _Weissman lab: http://weissmanlab.ucsf.edu
.. _demo dataset part one: https://www.dropbox.com/s/abktvrngn1lnzpb/plastid_demo.tar.bz2?dl=0
.. _demo dataset part two: https://www.dropbox.com/s/43xsvu7dz00k3q0/plastid_demo_part2.tar.bz2?dl=0
.. _test dataset: https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=0
