1	Original mapping provided by Array Vendor	Vendor mapping	1	\N
2	Raw value	Raw value	1	\N
3	Generalised log transformation based on VSN variance stabilised scores	VSN_GLOG	1	\N
6	Remapping to new assembly performed by LiftOver	LiftOver	1	\N
7	Hidden Markov Model based predictions based on tiling array data	Nessie (TilingHMM)	1	\N
8	Ratio generated by standard Sanger PCR array processing	SangerPCR	1	\N
11	Solexa clusters	Parzen	1	\N
12	Solexa clusters from wiggle data	Parzen	1	\N
13	Custom hit list	HitList	1	\N
15	Co-occurrence of overlapping feature types	Co-occurrence Overlap	1	\N
16	{'reg_feats' => 'Features from <a href="http://www.ensembl.org/info/docs/funcgen/index.html" class="cp-external">Ensembl Regulatory Build</a>.', 'core' => 'Sites enriched for marks of open chromatin (e.g. DNase1) or transcription factor binding sites.  Used to define the Regulatory Feature core regions in the <a href="http://www.ensembl.org/info/docs/funcgen/index.html" class="cp-external">Ensembl Regulatory Build</a>.', 'non_core' =>  'Sites enriched for histone modifications or polymerase binding.  Used to define Regulatory Feature bound regions in the <a href="http://www.ensembl.org/info/docs/funcgen/index.html" class="cp-external">Ensembl Regulatory Build</a>.'}	Regulatory Build	1	{'type' => 'fg_regulatory_features', 'name' => 'Reg. Feats',  'display' =>'off', 'depth' => 10, 'default' => {'contigviewbottom' => 'normal', 'generegview' => 'normal'} }
67	<a href="http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index">Tarbase</a> miRNA target predictions	TarBase	1	{'type' => 'mirna_targets', 'colourset' => 'synteny', 'display' =>'off'}
18	cisRED motif search (www.cisred.org)	cisRED	1	{'type' => 'regulatory_regions', 'colourset' => 'synteny', 'display' =>'off'}
19	VISTA Enhancer Assay (http://enhancer.lbl.gov/)	VISTA	1	{'type' => 'regulatory_regions', 'colourset' => 'synteny', 'display' =>'off'}
22	Weighted mean standardisation using the one step Tukey Biweight algorithm	Tukey Biweight	1	\N
26	Transcript alignments for ILLUMINA_WG arrays	ILLUMINA_WG_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
25	Genomic alignments for ILLUMINA_WG arrays	ILLUMINA_WG_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
27	Microarray probes from manufacturers are aligned to the genome by Ensembl, if the probe sequences are provided. The mapping is a two-step procedure outlined <a href="http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html">here</a>.	Probe2Transcript Annotation	0	undef
14	Hidden Markov Model based predictions based on tiling array data	HMM predictions based on tiling array data	1	{'type' => 'ctcf', 'name' => 'CTCF', 'display' => 'off', 'renderers' => {'off' => 'Off',  'tiling' => 'Normal'} }
31	Genomic alignments for AFFY_UTR arrays	AFFY_UTR_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
28	Transcript alignments for AFFY_UTR arrays	AFFY_UTR_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
30	Genomic alignments for AFFY_ST arrays	AFFY_ST_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
29	Transcript alignments for AFFY_ST arrays	AFFY_ST_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
34	Genomic alignments for CODELINK arrays	CODELINK_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
32	Genomic alignments for AGILENT arrays	AGILENT_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
36	Transcript alignments for AGILENT arrays	AGILENT_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
33	Genomic alignments for PHALANX arrays	PHALANX_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
35	Transcript alignments for PHALANX arrays	PHALANX_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
41	SWEmbl Peak Caller	SWEmbl	1	\N
42	SWEmbl Peak Caller	SWEmbl	1	\N
24	SWEmbl Peak Caller	SWEmbl	1	\N
23	SWEmbl Peak Caller	SWEmbl	1	\N
43	BWA single read alignment	BWA	1	\N
45	Filtered subset of Jaspar and Transfac TFBS PWM mappings	TFBS Motifs	1	\N
46	SWEMBL Peak Caller	SWEmbl	1	\N
47	SWEMBL Peak Caller	SWEmbl	1	\N
10	Genomic alignments for arrays	AlignProbe	0	\N
37	Transcript alignments for CODELINK arrays	CODELINK_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display'  =>'off' }
44	SWEMBL Peak Caller tuned for DNase1	SWEmbl	1	\N
50	Transcript alignments for ILLUMINA_INFINIUM arrays	ILLUMINA_INFINIUM_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display'  =>'off' }
48	Manual Annotation	Manual Annotation	1	\N
49	Import from Jaspar	Jaspar Matrix	1	\N
51	CCAT Peak Caller	CCAT	1	\N
53	K562 Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	K562 Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_K562' }
54	GM12878 Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	GM12878 Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_GM12878' }
55	H1ESC Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	H1ESC Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_H1ESC' }
56	HeLa-S3 Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	HeLa-S3 Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_HeLa-S3' }
57	HepG2 Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	HepG2 Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_HepG2' }
58	HUVEC Merge ENCODE segmentation state analysis (<a href="/info/docs/funcgen/regulatory_segmentation.html">segway/chromhmm</a>)	HUVEC Regulatory Segmentation	1	{'type' =>'fg_segmentation_features', 'colourset' => 'fg_segmentation_features','display'  =>'off', key=>'seg_HUVEC' }
60	Whole Genome Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates.	WGBS	1	{}
59	Reduced Representation Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates, filtered for a minimum of 10 reads	RRBS	1	{}
69	SWEmbl Peak Caller with IDR peak filtering	SWEMBL IDR	1	\N
70	Position Frequency Matrices from the <a href='http://jaspar.genereg.net/'>Jaspar Database</a> (5.0)	Jaspar	0	\N
80	Reduced Representation Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates and 0.0001 false discovery rate.	RRBS	1	{}
79	Whole Genome Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates and 0.0001 false discovery rate.	WGBS	1	{}
72	<a href="http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index">Tarbase</a> miRNA target predictions	TarBase	1	{'type' => 'mirna_targets', 'colourset' => 'synteny', 'display' =>'off'}
71	<a href="http://fantom.gsc.riken.jp/5/">Fantom 5</a> TSS/Enhancer Predictions	Fantom 5	1	{'type' => 'regulatory_regions', 'colourset' => 'fantom', 'display' =>'off', 'priority' => ['FANTOM robust enhancer'] }
73	ChromHMM 25-state segmentation of Blueprint human blood datasets	ChromHMM/Blueprint	1	{}
77	Segway 25-state segmentation of ENCODE and Roadmap Epigenomics human cell line datasets	Segway/ENCODE & Roadmap	1	{}
78	Segway 25-state segmentation of ENCODE and Roadmap Epigenomics human cell line datasets	Segway/ENCODE & Roadmap	0	{}