About: hapFabia is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data. It detects 100 times smaller segments than previous methods.

o citation update

o plot function improved

About: hapFabia is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data.

o citation update

o plot function improved

About: FABIA is a biclustering algorithm that clusters rows and columns of a matrix simultaneously. Consequently, members of a row cluster are similar to each other on a subset of columns and, analogously, members of a column cluster are similar to each other on a subset of rows. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. Applications include detection of transcriptional modules in gene expression data and identification of haplotypes/>identity by descent< consisting of rare variants obtained by next generation sequencing.

CHANGES IN VERSION 2.8.0

NEW FEATURES

o rescaling of lapla
o extractPlot does not plot sorted matrices

CHANGES IN VERSION 2.4.0

o spfabia bugfixes

CHANGES IN VERSION 2.3.1

NEW FEATURES

o Getters and setters for class Factorization

2.0.0:

• spfabia: fabia for a sparse data matrix (in sparse matrix format) and sparse vector/matrix computations in the code to speed up computations. spfabia applications: (a) detecting >identity by descent< in next generation sequencing data with rare variants, (b) detecting >shared haplotypes< in disease studies based on next generation sequencing data with rare variants;
• fabia for non-negative factorization (parameter: non_negative);
• changed to C and removed dependencies to Rcpp;
• improved update for lambda (alpha should be smaller, e.g. 0.03);
• introduced maximal number of row elements (lL);
• introduced cycle bL when upper bounds nL or lL are effective;
• reduced computational complexity;
• bug fixes: (a) update formula for lambda: tighter approximation, (b) corrected inverse of the conditional covariance matrix of z;

1.4.0:

• New option nL: maximal number of biclusters per row element;
• Sort biclusters according to information content;
• Improved and extended preprocessing;
• Update to R2.13

About: PSVM - Support vector classification, regression and feature extraction for non-square dyadic data, non-Mercer kernels.

Initial Announcement on mloss.org.

About: Implementation of LSTM for biological sequence analysis (classification, regression, motif discovery, remote homology detection). Additionally a LSTM as logistic regression with spectrum kernel is included.

Spectrum LSTM package included