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Update all the dead genes.mit.edu links in the documentation page #145

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36 changes: 18 additions & 18 deletions docs/source/index.rst
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Expand Up @@ -1551,26 +1551,26 @@ General reading on probabilistic modeling and inference
.. _SAM: http://samtools.sourceforge.net/SAM1.pdf
.. _GFF: http://www.sequenceontology.org/gff3.shtml
.. _GTF2GFF: http://www.sequenceontology.org/resources/converter_readme.html
.. _gtf2gff3.pl: http://genes.mit.edu/burgelab/miso/scripts/gtf2gff3.pl
.. _ucsc_table2gff3.pl: http://genes.mit.edu/burgelab/miso/scripts/ucsc_table2gff3.pl
.. _gtf2gff3.pl: http://hollywood.mit.edu/burgelab/miso/scripts/gtf2gff3.pl
.. _ucsc_table2gff3.pl: http://hollywood.mit.edu/burgelab/miso/scripts/ucsc_table2gff3.pl
.. _genePredToGtf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
.. _biotoolbox: http://code.google.com/p/biotoolbox/
.. _Drosophila melanogaster alternative events (modENCODE): http://genes.mit.edu/burgelab/miso/annotations/modENCODE_alt_events.zip
.. _Events to genes mapping for mm9: http://genes.mit.edu/burgelab/miso/annotations/mm9_events_to_genes.zip
.. _Events to genes mapping for hg18: http://genes.mit.edu/burgelab/miso/annotations/hg18_events_to_genes.zip
.. _Events to genes mapping for hg19: http://genes.mit.edu/burgelab/miso/annotations/hg19_events_to_genes.zip
.. _mm9 ensGene GFF annotation: http://genes.mit.edu/burgelab/miso/annotations/ucsc_tables/mm9/ensGene.gff3
.. _mm10 ensGene GFF annotation: http://genes.mit.edu/burgelab/miso/annotations/ucsc_tables/mm10/ensGene.gff3
.. _hg18 ensGene GFF annotation: http://genes.mit.edu/burgelab/miso/annotations/ucsc_tables/hg18/ensGene.gff3
.. _hg19 ensGene GFF annotation: http://genes.mit.edu/burgelab/miso/annotations/ucsc_tables/hg19/ensGene.gff3
.. _Mouse genome (mm9) alternative events: http://genes.mit.edu/burgelab/miso/annotations/mm9_alt_events.zip
.. _Human genome (hg18) alternative events: http://genes.mit.edu/burgelab/miso/annotations/hg18_alt_events.zip
.. _Human genome (hg19) alternative events: http://genes.mit.edu/burgelab/miso/annotations/hg19_alt_events.zip
.. _3′READS annotations for (mm9) mouse genome (.zip): http://genes.mit.edu/burgelab/miso/annotations/tian_apa_events.zip
.. _Mus_musculus.NCBIM37.65.gff: http://genes.mit.edu/burgelab/miso/annotations/gene-models/Mus_musculus.NCBIM37.65.gff.zip
.. _Mus_musculus.NCBIM37.65.with_chr.gff: http://genes.mit.edu/burgelab/miso/annotations/gene-models/Mus_musculus.NCBIM37.65.with_chr.gff.zip
.. _Homo_sapiens.GRCh37.65.gff: http://genes.mit.edu/burgelab/miso/annotations/gene-models/Homo_sapiens.GRCh37.65.gff.zip
.. _Homo_sapiens.GRCh37.65.with_chr.gff: http://genes.mit.edu/burgelab/miso/annotations/gene-models/Homo_sapiens.GRCh37.65.with_chr.gff.zip
.. _Drosophila melanogaster alternative events (modENCODE): http://hollywood.mit.edu/burgelab/miso/annotations/modENCODE_alt_events.zip
.. _Events to genes mapping for mm9: http://hollywood.mit.edu/burgelab/miso/annotations/mm9_events_to_genes.zip
.. _Events to genes mapping for hg18: http://hollywood.mit.edu/burgelab/miso/annotations/hg18_events_to_genes.zip
.. _Events to genes mapping for hg19: http://hollywood.mit.edu/burgelab/miso/annotations/hg19_events_to_genes.zip
.. _mm9 ensGene GFF annotation: http://hollywood.mit.edu/burgelab/miso/annotations/ucsc_tables/mm9/ensGene.gff3
.. _mm10 ensGene GFF annotation: http://hollywood.mit.edu/burgelab/miso/annotations/ucsc_tables/mm10/ensGene.gff3
.. _hg18 ensGene GFF annotation: http://hollywood.mit.edu/burgelab/miso/annotations/ucsc_tables/hg18/ensGene.gff3
.. _hg19 ensGene GFF annotation: http://hollywood.mit.edu/burgelab/miso/annotations/ucsc_tables/hg19/ensGene.gff3
.. _Mouse genome (mm9) alternative events: http://hollywood.mit.edu/burgelab/miso/annotations/mm9_alt_events.zip
.. _Human genome (hg18) alternative events: http://hollywood.mit.edu/burgelab/miso/annotations/hg18_alt_events.zip
.. _Human genome (hg19) alternative events: http://hollywood.mit.edu/burgelab/miso/annotations/hg19_alt_events.zip
.. _3′READS annotations for (mm9) mouse genome (.zip): http://hollywood.mit.edu/burgelab/miso/annotations/tian_apa_events.zip
.. _Mus_musculus.NCBIM37.65.gff: http://hollywood.mit.edu/burgelab/miso/annotations/gene-models/Mus_musculus.NCBIM37.65.gff.zip
.. _Mus_musculus.NCBIM37.65.with_chr.gff: http://hollywood.mit.edu/burgelab/miso/annotations/gene-models/Mus_musculus.NCBIM37.65.with_chr.gff.zip
.. _Homo_sapiens.GRCh37.65.gff: http://hollywood.mit.edu/burgelab/miso/annotations/gene-models/Homo_sapiens.GRCh37.65.gff.zip
.. _Homo_sapiens.GRCh37.65.with_chr.gff: http://hollywood.mit.edu/burgelab/miso/annotations/gene-models/Homo_sapiens.GRCh37.65.with_chr.gff.zip
.. _Bowtie: http://bowtie-bio.sourceforge.net/
.. _Tophat: http://tophat.cbcb.umd.edu/
.. _IGV: http://www.broadinstitute.org/igv/
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