Man pages for dieterich-lab/JACUSA2helper
Post-processing for JACUSA2 output
| add_arrest_rate | Add arrest rate. |
| All | Merge tibbles with columns holding logical values with AND to... |
| Allnum | Merge tibbles with columns holding the sum of numeric values... |
| Any | Merge tibbles with columns holding logical values with OR to... |
| arrest_rate | Calculate arrest rate. |
| base_call | Observed base calls. |
| base_count | Retrieves the total number of observed unique bases. |
| base_ratio | Calculate base call ratios for base counts. |
| base_sub | Calculates reference base to base call (base substitution). |
| clean_tag | Transform read substitution. |
| coverage | Calculate coverage for structured column. |
| create_data | Create data matrix for NMF |
| DARTseq | DART-seq from Meyer 2019 |
| expand_tag | Expand tagged reads |
| extend | Extend site. |
| fast_unpack_info | Fast unpack info. |
| filter_artefact | Filters sites by artefacts. |
| gather_repl | Extract values from a structured column. |
| get_info_keys | Get keys of info field. |
| get_motif | Get sequence |
| HIVRT_call2 | JACUSA2 output for call-2 on HIVRT condition in Zhou et. al... |
| HIVRT_rt_arrest | JACUSA2 output for rt-arrest on HIVRT condition in Zhou et.... |
| id | Merged coordinate information |
| is_DRACH | Check if DRACH motif. |
| JACUSA2helper | JACUSA2helper: A package for post-processing JACUSA2 result... |
| lapply_cond | Apply f to all conditions |
| lapply_repl | Apply f to all replicates |
| learn_nmf | Estimate factorization rank from JACUSA2 output |
| m6a_miclip | m6a predictions from 3 miCLIP experiments |
| m6a_nmf_reduced | Non-negative matrix factorization on m6a predictions from 3... |
| m6a_nmf_results | Non-negative matrix factorization on m6a predictions from 3... |
| mapply_repl | Apply f to all replicates |
| mask_sub | Mask a set of base substitutions. |
| max_observed_bc | Calculates most frequent base calls |
| MazF_FTO | MazF_FTO from Zhang et al. 2019 |
| merge_sub | Merges base substitutions. |
| non_ref_ratio | Calculate non reference ratio from base counts and reference... |
| observed_bc | Calculates observed base calls |
| predict_mods | Predict modifications in JACUSA2 output |
| rdd | Subset of RDDs detected by JACUSA2 in HEK-293 untreated cells |
| read_result | Read JACUSA2 result file |
| read_results | Read multiple related JACUSA2 results |
| reduce_coef | Reduce coefficient matrix |
| rnam | rRNA modification map of rRNAs according to Taika et al. |
| robust | Check if data is robust |
| rrd | Subset of RRDs detected by JACUSA2 in HEK-293 ADAR KD and... |
| SIIIRTMg_call2 | JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et.... |
| SIIIRTMg_rt_arrest | JACUSA2 output for rt-arrest on SIIIRTMg condition in Zhou... |
| SIIIRTMn_call2 | JACUSA2 output for call-2 on SIIIRTMn condition in Zhou et.... |
| SIIIRTMn_rt_arrest | JACUSA2 output for rt-arrest on SIIIRTMn condition in Zhou... |
| sub_counts | Calculates base substitution counts |
| sub_ratio | Calculates base substitution ratio (e.g.: editing frequency). |
| unpack_info | Unpack info field |
| variant_bc | Calculates non-reference base calls |
| write_bedGraph | Writes vector of values as bedGraph file. |
| Zhou2018_call2 | Combined JACUSA2 output for call-2 on all conditions in Zhou... |
| Zhou2018_rt_arrest | Combined JACUSA2 output for rt-arrest on all conditions in... |
