cmd/

animateunjitter removes lines from a sorted manifest in a fashion that avoids returning to a previously seen series_number.

bimmanglesnpids is designed to handle a specific situation where you want to mangle rsids intentionally.

Convert BOLT-LMM input into input satisfactory for ldhub

clinvar2bigquery is designed to take clinvar data, filter it using criteria that are useful to my line of work, and then format it so that it can be ingested in bigquery.

Deletes files from `folder` not matching names found in `permitted-list`, with `suffix` optionally being appended to `permitted-list` to facilitate matching.

dicom-mip produces maximum intensity projections, as well as average intensity projections and .mp4 videos of the projections through the 3D block of voxels from sagittal and coronal projections.

dicom2las converts DICOM files to LAS files (LASer format), which is a [format for point clouds](https://en.wikipedia.org/wiki/LAS_file_format).

MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.

gtf2tsv flattens a gtf file to a tsv seems to require a 2-pass approach

MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.

nearbygenes finds all genes whose transcript start sites are within a given radius of a given chr:pos.

nearestgene finds the single gene whose transcript start site is closest to a given chr:pos.

pixeloverlap computes overlap/agreement metrics between two images drawn with an encoding compatible with the overlay.LabeledPixelToID function.

pixeloverlapsummary is a convenience tool to summarize the output of pixeloverlap by label

colqc performs qc on columnar data (the output of pixelcounter)

pixelreplace replaces specific pixel-label IDs from the overlay package with specified replacement labels.

pngreplace replaces specific pixel-labels from the overlay package with specified replacement labels.

pngupsample ingests a PNG and parameters that indicate (1) how to resize pixels and (2) which subset of the image to upsample, then produces the subsetted, upsampled PNG.