clonalExpansion |
Clonally expands the simulated repertoire generated from fullRepertoire function. |
fullRepertoire |
Simulates full heavy chain antibody repertoires for either human or mice. |
hotspot_df |
hotspot_df |
ighd_hum_df |
ighd_hum_df |
ighd_mus_df |
ighd_mus_df |
ighj_hum_df |
ighj_hum_df |
ighj_mus_df |
ighj_mus_df |
ighv_hum_df |
ighv_hum_df |
ighv_mus_df |
ighv_mus_df |
igkj_hum_df |
igkj_hum_df |
igkj_mus_df |
igkj_mus_df |
igkv_hum_df |
igkv_hum_df |
igkv_mus_df |
igkv_mus_df |
iglj_hum_df |
iglj_hum_df |
iglj_mus_df |
iglj_mus_df |
iglv_hum_df |
iglv_hum_df |
iglv_mus_df |
iglv_mus_df |
one_spot_df |
one_spot_df |
repertoireFastas |
Converts AbSim's output sequences and names into fasta file format. Each tree within the repertire will be stored in an individual fasta file. Utilizes sink() and cloneAllConnections() from R base |
singleLineage |
Antibody lineage simulations using only one set of V(D)J germline genes. The main difference between this function and the fullRepertoire function is that there can be multiple VDJ recombination events within one tree. Each VDJ recombination event in the singleLineage function is a branching event within the existing tree, whereas the VDJ recombination events in the fullRepertoire function start a new tree. |