Man pages for Pinlyu3/LRLoop
Two-way communication between cells
| apply_hub_corrections_noligand | Downweight the hub nodes in the signaling and gene regulatory... |
| Circos_plot | Circos plot |
| Circos_plot_2 | Circos plot 2 |
| construct_receptor_target_matrix | Construct a matrix containing receptor-target regulatory... |
| construct_receptor_tf_matrix | Construct a matrix containing receptor-tf probability scores |
| construct_tf_target_matrix_noligand | Convert gene regulatory network into a matrix. |
| get_DEG | Identify the differentially expressed genes and the... |
| get_expr_lr | Identify "expressed" ligand-receptor pairs |
| get_LRL | Get the LRloop L1_R1-L2_R2 pairs |
| getLRLoopPartnerInfo | Get the number and list of LRLoop partners of LRpairs of... |
| get_LRscores | Calculate the LRscore of each "expressed" ligand-receptor... |
| getLRscoreupdated_cutoff | Calculate an LRscores_LRL-cutoff based on the distribution of... |
| getnLRloops_rand | Construct a specified number of random LRloop networks... |
| get_pct_expr | Calculate the gene detection rate in each condition |
| L1R1L2R2Score | Calculate the LRloop score of a L1-R1_L2-R2 pair |
| L1R1L2R2ScoreHill | L1R1L2R2ScoreHill |
| LRL_info_collection | Collect data on LRloop network relevant ligands and receptors |
| LRL_stats | Calculate some basic statistics on LRloops |
| LRscore | Calculate the LRscore of an L-R pair |
| make_discrete_ligand_target_matrix_general | Identify the targets of each ligand's cognate receptors (1:... |
| make_LRL_list | Find the regulatory relationships of all the (L2-R2)-(L1-R1)... |
| MostBasicLRinfo | Print: Number of L1-R1 pairs Number of L1 Number of R1 Number... |
| plotLRL | Plot the LRloop network (A_ and B_ in the LR node lables:... |
| PrepareBasics | Get a list of some basic data info |
| print_LRL_Score_options | Print available options for the function "plotLRL" variable... |
| take_LR_expr_score | Create a dataframe for the expr_scores of L1R1 or L2R2 pairs... |
| takeNicheNetScores | Put ligand/receptor_activity scores for expressed... |
| updateLRscores | Modify the LRscores of the LRs expressed from ct1 to ct2... |
| updateLRscores_rand | Get modified LRscores with random LRloop networks |
| writeLRL | Write the LRloop_info into .csv files |
