celloracle.data module¶
The
datamodule implements data download and loading.
celloracle.data.load_Celegans_promoter_base_GRN(version='ce10_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_Pig_promoter_base_GRN(version='Sscrofa11.1_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_Scerevisiae_promoter_base_GRN(version='sacCer3_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_TFinfo_df_mm9_mouse_atac_atlas(version='0.10.0', force_download=False)¶Load Transcription factor binding information made from mouse scATAC-seq atlas dataset. mm9 genome was used for the reference genome.
Args:
- Returns
TF binding info.
- Return type
pandas.dataframe
celloracle.data.load_chicken_promoter_base_GRN(version='galGal6_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_drosophila_promoter_base_GRN(version='dm6_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_human_promoter_base_GRN(version='hg19_gimmemotifsv5_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_mouse_promoter_base_GRN(version='mm10_gimmemotifsv5_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_rat_promoter_base_GRN(version='rn6_gimmemotifsv5_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_tutorial_links_object(version='0.10.0', force_download=False)¶
celloracle.data.load_tutorial_oracle_object(version='0.10.0', force_download=False)¶
celloracle.data.load_xenopus_tropicalis_promoter_base_GRN(version='xenTro3_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe
celloracle.data.load_zebrafish_promoter_base_GRN(version='danRer11_CisBPv2_fpr2', force_download=False)¶Load Base GRN made from promoter DNA sequence and motif scan.
Args:
- Returns
Base GRN as a matrix.
- Return type
pandas.dataframe