Man pages for TaliaferroLab/FeatureReachR
Extract Enriched Biological Features From RNA-seq Data
| case_genes | List of "case" mouse gene IDs |
| CISBPRNA_hs_PWM | CISBPRNA Homo sapiens PWM list |
| CISBPRNA_mm_PWM | CISBPRNA Mus muscululs PWM list |
| compares | Compare the average Length or GC content of two DNAStringSet... |
| ctrl_genes | List of "control" mouse gene IDs |
| custom_PWM_list | custom PWM list examlpe |
| estimate_motif_from_kmer | Estimate Motif Occurance from Kmers |
| filter_Tx | Filter out undesired transcripts from gencode gff files |
| gene2Tx | Get transcript list from gene list |
| get_ctrl_tx | Get Control Transcript list from Case gene list |
| getTxOut | Export sequence of interest from a TxDb object |
| hello | Hello, World! |
| kmer_by_gene | Count Kmers within each sequence of a DNAStringSet |
| kmer_compare | Compare kmer content between two DNAStringSets |
| make_length_df | Create transcript length reference dataframe |
| motif_by_gene | Count Motif occurances within each sequence of a DNAStringSet |
| motif_compare | Compare Motif occurances between two DNAStringSets |
| Plots | Group Kmers and Represent them as Motif Logos |
| RBFOX2_cisbpRNA_compare | cisbpRNA motif comparisions for RBFOX2 data |
| RBFOX2_RBNS_compare | RBNS motif comparisions for RBFOX2 data |
| RBNS_PWM | RNA Bind and Seq PWM list |
| relate_kmer_PWM | Relate Kmers and PWM list |
| retrieves | Get length or GC of each sequence in a DNAStringSet object |
| RNA_breakdown | Summarize RNA types in transcript list |
