aRxiv |
Counts of the aRxiv field categories of 4 UChicago Statistics professors. A dataset of compositional counts of 10 aRxiv field categories for 4 professors' publications in aRxiv. |
EBF1_disc1 |
EBF1_disc1 transcription factor position weight matrix A dataset of composition probabilities of A, C, G and T in 10 positions of the motif. |
GetConsensusSeq |
Function for obtaining consensus sequence of DNA sequence symbols from a PWM matrix |
get_logo_heights |
Get heights of logos in nlogomaker() under different scoring schemes |
get_viewport_logo |
Function for creating a multi-panel logo viewport |
himalayan_fauna |
Proportional abundances of different bird species in the Himalayan mountains A dataset of proportional composition of 140 bird species in 3 regions of the Himalayas. |
histone_marks |
Compositional data of histone marks in different regions of genome along with background information A list containing two matrices storing composition of 5 histone marks (H3K4ME1, H3K4ME2, H3K4ME3, H3AC, H4AC) in 5 regions of the genome |
logomaker |
Create logo plots from aligned sequences or positional frequency (weight) matrix |
logo_pssm |
Function to plot PSSM logo plot visualization. |
makemylogo |
Logo maker for a given English alphanumeric with common punctuations |
mutation_sig |
Compositional mutational signature data, with mismatch and flanking base frequencies reported A dataset of compositional weights for mismatches in the "0"the position (center of signature) and that of the bases A, C, G, T for two left flanking bases (-1, -2) and two right flanking bases (1, 2). |
nlogomaker |
Main workhorse function that builds negative logo plots |
pssm |
Position specific scoring matrix data A dataset of position specific sores of various amino acids in 9 positions binding domain. |
seqlogo_example |
An example of the position weight matrix taken from seqLogo package A dataset of composition probabilities of A, C, G and T in 8 positions of the motif. |
UMI |
An example of the position weight matrix of the bases in the first 30 positions from ends of sequenced reads (together with the barcode) A dataset of composition probabilities of A, C, G and T in 30 positions from the 5' end of reads. |