Man pages for AnnikaGable/chromium
Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

bin_chromBin an existing InteractionSet
chr2Hi-C interaction data for chromosome 2 of mouse stem cells
Create_any_resolution_LFMCreate a ligation frequency matrix or InteractionSet binned...
easy_Iset_to_LFMConvert an InteractionSet into a sparse, upper triangle...
import_chromRead preprocessed genomic interaction files into an...
IPF_algIterative proportional fitting algorithm
Iset_region_to_LFMConvert an InteractionSet region into a ligation frequency...
Iset_to_LFMConvert an InteractionSet object into a ligation frequency...
LFM_to_IsetConvert a sparse ligation frequency matrix into an...
loss_functionLoss function
normalize_chromNormalize an InteractionSet with iterative proportional...
normalize_LFM_iterativelyNormalize a ligation frequency matrix with iterative...
pairID_to_RFpairDecode the pair ID into the bin pairs or restriction fragment...
plot_qaOutput a quality assessment report.
quality_assessmentQuality assessment of whole genome Hi-C data.
read_bed_rafRead preprocessed genomic interaction files to produce RFanno...
RFpairs_to_IsetConvert restriction fragment annotation and restriction...
RFpair_to_pairIDEncode a restriction fragment pair or bin pair into one...
rotated_imagePlot a rotated and, if required, smoothed interaction matrix.
subset_chromChoose a chromosome and a region within which InteractionSet...
subset_interactionsChoose a chromosome and a range within which InteractionSet...
sym_to_triangleConvert a sparse symmetric matrix to a sparse triangle...
triangle_to_symConvert a sparse triangle matrix to a sparse symmetric...
visualize_chromTriangle visualization of Hi-C data with tracks for chipseq,...
AnnikaGable/chromium documentation built on May 28, 2017, 4:53 p.m.