Multi-Purpose and Flexible k-Meric Enrichment Analysis Software
Add transparency to color.
Convert a BED file to chromosome-separated csv files.
Build control regions
Count k-mers from given sequence(s) and build a data.table of k-mer co...
Count k-mers with specified middle pattern from given sequence(s) and ...
Count kmers from a sequence in given ranges and build a data.table of ...
Function constructs a URL for a REST API call by appending query param...
Function calculates the skew of k-mers based on their occurrence in po...
Calculate position weight matrix of overlapping sequences. Simulation ...
Function prints a given message in a formatted header with borders.
Loading, manipulating, and analyzing coordinate data.
Count sequence content in a given sequence.
Count sequence content in a given sequence.
Function performs an analysis of base composition including sequence f...
Function chops k-mers within specified ranges of a sequence and counts...
Function performs an analysis of the distribution of genomic cases.
Count k-mers from string(s) using a simple hash table.
Locate a middle sequence pattern and count its sequence context.
Count Relevant K-mers with Specified Middle Pattern from Sequence Stri...
Ccount sequence context of given point positions.
Count k-mers in given ranges of a sequence.
Count reverse complement sequence from its opposite strand. Build for ...
Count sequence content in a sliding window of a sequence.
Count sequence content in a sliding window of a sequence.
Function downloads genome fasta files from the NCBI FTP database. User...
Function downloads chromosome-separated fasta genome sequences from th...
Example 2-mer enrichment/depletion scores
Function generates various exploratory analyses.
Extract k-mers from a given Coordinate object and Genome objects
Function processes UCSC genePred tables to generate coordinates for va...
Resolve and generate genic element coordinates from UCSC genePred tabl...
Get COSMIC authenticated URL.
Get Cancer Gene Census (CGC) from COSMIC database.
Function retrieves the latest version information of the COSMIC databa...
Function downloads the latest Cosmic Mutant Export data from the COSMI...
A generic function to get Ensembl data persistently from a URL. This i...
Get features of a given region.
Get features of given variant IDs.
Get features of given variant IDs.
Get gnomAD VCF file using tabix.
Get Virus Metadata Resource (VMR) from International Committee on Taxo...
Get NCBI assembly summary.
Function calculates scores for k-mers based on case and control k-mer ...
Retrieve Gene Prediction Table from UCSC for a Given Genome
Read VCF metainfo file using tabix.
Initialise k-mer table with all possible k-mers
A R6 class wrapper for data.table
kmeRtone all-in-one user interface
Build Coordinate object.
Build Genome object.
Function calculates various genomic content metrics based on the provi...
Map k-mers of a given sequence and coordinate
Merge overlapping or continuous regions.
Mix color
Class constructor - build NCBI Genome object
Partition overlapping or continuous regions.
Download file until successful
Read a BED file. One-based indexing is enforced.
Read FASTA files.
Read VCF file using tabix.
Read VCF file using tabix.
Remove overlapping region in coordinate data.table.
Get reverse complement sequence of DNA
Calculate susceptibility scores for k-mers in case and control regions...
Function calculates the Z-score for each k-mer based on the observed c...
Select genomes for cross-species studies.
Select the best representative species from the NCBI assembly summary.
Simulate a population given ranges of chromosome sequence to mutate.
Split a FASTA file by header.
Study k-mer composition of selected COSMIC causal cancer genes across ...
Study k-mer composition across species.
Study k-mer composition of causal cancer genes from COSMIC Cancer Gene...
Study k-mer composition across species.
A system2 wrapper. If anything happen, just give me error!
Trim out-of-bound coordinates
Class constructor - build Genome object
Write a BED file. Zero-based indexing is enforced.
Write FASTA files.
Write VCF file and compress using bgzip.
A multi-purpose and flexible k-meric enrichment analysis software. 'kmeRtone' measures the enrichment of k-mers by comparing the population of k-mers in the case loci with a carefully devised internal negative control group, consisting of k-mers from regions close to, yet sufficiently distant from, the case loci to mitigate any potential sequencing bias. This method effectively captures both the local sequencing variations and broader sequence influences, while also correcting for potential biases, thereby ensuring more accurate analysis. The core functionality of 'kmeRtone' is the SCORE() function, which calculates the susceptibility scores for k-mers in case and control regions. Case regions are defined by the genomic coordinates provided in a file by the user and the control regions can be constructed relative to the case regions or provided directly. The k-meric susceptibility scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is highly flexible by allowing users to also specify their target k-mer patterns and quantify the corresponding k-mer enrichment scores in the context of these patterns, allowing for a more comprehensive approach to understanding the functional implications of specific DNA sequences on a genomic scale (e.g., CT motifs upon UV radiation damage). Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).