Function reference
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All() - Merge tibbles with columns holding logical values with AND to a vector.
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Allnum() - Merge tibbles with columns holding the sum of numeric values of a vector.
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Any() - Merge tibbles with columns holding logical values with OR to a vector.
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DARTseq - DART-seq from Meyer 2019
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HIVRT_call2 - JACUSA2 output for call-2 on HIVRT condition in Zhou et. al 2018 data
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HIVRT_rt_arrest - JACUSA2 output for rt-arrest on HIVRT condition in Zhou et. al 2018 data
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JACUSA2helper - JACUSA2helper: A package for post-processing JACUSA2 result files.
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MazF_FTO - MazF_FTO from Zhang et al. 2019
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SIIIRTMg_call2 - JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et. al 2018 data
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SIIIRTMg_rt_arrest - JACUSA2 output for rt-arrest on SIIIRTMg condition in Zhou et. al 2018 data
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SIIIRTMn_call2 - JACUSA2 output for call-2 on SIIIRTMn condition in Zhou et. al 2018 data
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SIIIRTMn_rt_arrest - JACUSA2 output for rt-arrest on SIIIRTMn condition in Zhou et. al 2018 data
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Zhou2018_call2 - Combined JACUSA2 output for call-2 on all conditions in Zhou et. al 2018 data
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Zhou2018_rt_arrest - Combined JACUSA2 output for rt-arrest on all conditions in Zhou et. al 2018 data
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add_arrest_rate() - Add arrest rate.
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arrest_rate() - Calculate arrest rate.
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base_call() - Observed base calls.
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base_count() - Retrieves the total number of observed unique bases.
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base_ratio() - Calculate base call ratios for base counts.
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base_sub() - Calculates reference base to base call (base substitution).
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clean_tag() - Transform read substitution.
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coverage() - Calculate coverage for structured column.
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create_data() - Create data matrix for NMF
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expand_tag() - Expand tagged reads
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extend() - Extend site.
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fast_unpack_info() - Fast unpack info.
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filter_artefact() - Filters sites by artefacts.
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gather_repl() - Extract values from a structured column.
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get_info_keys() - Get keys of info field.
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get_motif() - Get sequence
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id() - Merged coordinate information
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is_DRACH() - Check if DRACH motif.
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lapply_cond() - Apply f to all conditions
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lapply_repl() - Apply f to all replicates
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learn_nmf() - Estimate factorization rank from JACUSA2 output
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m6a_miclip - m6a predictions from 3 miCLIP experiments
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m6a_nmf_results - Non-negative matrix factorization on m6a predictions from 3 miCLIP experiments
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m6a_nmf_results - Non-negative matrix factorization on m6a predictions from 3 miCLIP experiments
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mapply_repl() - Apply f to all replicates
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mask_sub() - Mask a set of base substitutions.
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max_observed_bc() - Calculates most frequent base calls
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merge_sub() - Merges base substitutions.
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non_ref_ratio() - Calculate non reference ratio from base counts and reference base.
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observed_bc() - Calculates observed base calls
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predict_mods() - Predict modifications in JACUSA2 output
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rdd - Subset of RDDs detected by JACUSA2 in HEK-293 untreated cells
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read_result() - Read JACUSA2 result file
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read_results() - Read multiple related JACUSA2 results
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reduce_coef() - Reduce coefficient matrix
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rnam - rRNA modification map of rRNAs according to Taika et al.
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robust() - Check if data is robust
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rrd - Subset of RRDs detected by JACUSA2 in HEK-293 ADAR KD and untreated cells
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sub_counts() - Calculates base substitution counts
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sub_ratio() - Calculates base substitution ratio (e.g.: editing frequency).
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unpack_info() - Unpack info field
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variant_bc() - Calculates non-reference base calls
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write_bedGraph() - Writes vector of values as bedGraph file.