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thibautjombart
adegenet:Exploratory Analysis of Genetic and Genomic Data
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Maintained by Zhian N. Kamvar. Last updated 2 months ago.
182 stars 12.60 score 1.9k scripts 29 dependents
henrikbengtsson
PSCBS:Analysis of Parent-Specific DNA Copy Numbers
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
7 stars 7.63 score 34 scripts 9 dependents
bioc
ChIPanalyser:ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.
Maintained by Patrick C.N. Martin. Last updated 5 months ago.
softwarebiologicalquestionworkflowsteptranscriptionsequencingchiponchipcoveragealignmentchipseqsequencematchingdataimportpeakdetection
4.38 score 12 scripts