GitHub - js2264/HiContactsData: HiContacts companion data package (original) (raw)

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HiContactsData

HiContactsData is a companion data package giving programmatic access to several processed Hi-C files for demonstration, such as cool, mcool and pairs files. It is meant to be used with HiContacts.

The only function provided by HiContactsData package is HiContactsData(). Several files are avaible using this function, namely:

• From Bastie, Chapard et al., Nature Structural & Molecular Biology 2022:
  • S288C fastq files (R1 & R2) (sample: yeast_wt, format = fastq_R{12})
  • S288C HiCool processing log (sample: yeast_wt, format = HiCool_log)
  • S288C.cool (sample: yeast_wt, format = cool)
  • S288C.mcool (sample: yeast_wt, format = mcool)
  • S288C_G1.mcool (sample: yeast_g1, format = mcool)
  • S288C_G2M.mcool (sample: yeast_g1, format = mcool)
  • S288C_G1.pairs (sample: yeast_g2m, format = pairs)
  • S288C_G2M.pairs (sample: yeast_g2m, format = pairs)
  • S288C.hic (sample: yeast_wt, format = hic)
  • S288C.hicpro.matrix (sample: yeast_wt, format = hicpro_matrix)
  • S288C.hicpro.bed (sample: yeast_wt, format = hicpro_bed)
  • S288C.pairs.gz for chrII only (sample: yeast_wt, format = pairs)
  • S288C_Eco1-AID.mcool (sample: yeast_Eco1, format = mcool)
  • S288C_Eco1-AID.pairs.gz for chrII only (sample: yeast_Eco1, format = pairs)
• From Bonev et al., Cell 2017:
  • mESCs.mcool (sample: mESCs, format = mcool)
  • mESCs.pairs.gz for chr13 only (sample: mESCs, format = pairs)
• From Krietenstein et al., Mol. Cell 2020:
  • microC_HFFc6_chr17.mcool (sample: microC, format = mcool)