Man pages for russHyde/reeq
Provides Some Helper Functions For RNA-Seq Analysis / IO
| append_feature_annotations | Add new columns from a table of feature-data into the... |
| as_sig_test_summary | as_sig_test_summary |
| cbind_feature_counts | Combine a list of feature-count 'data.frame's into a single... |
| compute_fitted_values | Obtain fitted values for a given combination of design... |
| cqn_dgelist | cqn_dgelist |
| define_contrasts | define a contrasts matrix based on a vector of string... |
| export | Export a data structure to a (set of) file(s) |
| export.sig_test_summary | Export a 'sig_test_summary' object to files |
| extract_cutadapt_summary | Extract the 'summary' section from the text from a cutadapt... |
| feature_counts_to_dgelist | Convert a 'data.frame' containing feature-count data into an... |
| filter_by_read_count | filter_by_read_count |
| get_features | Extract the features (genes) from an object |
| get_features.sig_test_summary | Extract the features from a sig_test_summary |
| get_gc_percent | Obtain the GC percentage for a set of genes from a biomaRt... |
| get_sig_test_summary | get_sig_test_summary |
| helper_check_validity_k_covered | Checks the validity of input to k-coverage functions |
| helper_k_covered_docs | runner_k_covered |
| import_contrasts | Import a contrasts matrix from a tab-separated file |
| import_cutadapt_summary | Extract the basepair/readpair counts from the 'summary'... |
| import_design | Obtain a design matrix from a file. |
| import_hisat2_summary | Extract the alignment summary statistics from a hisat2... |
| parse_colon_separated_lines | parse_colon_separated_lines |
| parse_cutadapt_summary | Takes the 'summary' text from a cutadapt log-file and... |
| parse_hisat2_summary | parse_hisat2_summary |
| parse_lrt_table | parse_lrt_table |
| parse_numeric_fields | parse_numeric_fields |
| read_feature_counts | Import read counts from a set of featureCounts files and... |
| read_single_feature_counts_file | Read a single featureCounts file |
| replace_with | replace_with |
| set_offset | Add (or replace) an offset matrix in DGEList |
| spread_and_rename_cutadapt_fieldnames | spread_and_rename_cutadapt_fieldnames |
| spread_and_rename_hisat2_fieldnames | spread_and_rename_hisat2_fieldnames |
| spread_and_rename_numeric_fields | spread_and_rename_numeric_fields |
| which_k_covered | Returns the row-index for those rows in a 'matrix' (or... |
| which_k_covered_across_samples | which_k_covered_across_samples |
| which_k_covered_each_sample | which_k_covered_each_sample |
