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bioc
QDNAseq:Quantitative DNA Sequencing for Chromosomal Aberrations
Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
Maintained by Daoud Sie. Last updated 5 months ago.
copynumbervariationdnaseqgeneticsgenomeannotationpreprocessingqualitycontrolsequencing
49 stars 10.10 score 177 scripts 4 dependentsbioc
ACE:Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.
Maintained by Jos B Poell. Last updated 5 months ago.
copynumbervariationdnaseqcoveragewholegenomevisualizationsequencing
15 stars 7.03 score 18 scriptsbioc
CGHcall:Calling aberrations for array CGH tumor profiles.
Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
Maintained by Mark van de Wiel. Last updated 5 months ago.
microarraypreprocessingvisualization
6.18 score 42 scripts 6 dependentsbioc
biscuiteer:Convenience Functions for Biscuit
A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.
Maintained by Jacob Morrison. Last updated 5 months ago.
dataimportmethylseqdnamethylation
6 stars 5.98 score 16 scriptsbioc
cfdnakit:Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).
Maintained by Pitithat Puranachot. Last updated 5 months ago.
copynumbervariationsequencingwholegenome
8 stars 5.20 score 8 scriptsbioc
GeneBreak:Gene Break Detection
Recurrent breakpoint gene detection on copy number aberration profiles.
Maintained by Evert van den Broek. Last updated 5 months ago.
acghcopynumbervariationdnaseqgeneticssequencingwholegenomevisualization
2 stars 4.60 score 6 scriptsbioc
CGHregions:Dimension Reduction for Array CGH Data with Minimal Information Loss.
Dimension Reduction for Array CGH Data with Minimal Information Loss
Maintained by Sjoerd Vosse. Last updated 5 months ago.
microarraycopynumbervariationvisualization
4.32 score 26 scriptsbioc
CGHnormaliter:Normalization of array CGH data with imbalanced aberrations.
Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).
Maintained by Bart P.P. van Houte. Last updated 5 months ago.
4.15 score 1 scripts