GALLO v2.0
- The GALLO v2.0 introduces new tools for pleiotropic effect detection, estimation of effective marker numbers and independent chromosomal segments, gene-level p-value calculation, and network-based visualization and gene prioritization. This is the most substantial update since GALLO’s initial release. These additions expand users’ ability to integrate high-throughput data, uncover hidden patterns across datasets, mine previously reported associations, and more efficiently investigate the genetic architecture of complex traits in livestock.


GALLO v1.5

- The functions to create the symmetric squared matrices for gene-level p-value and number of effective markers estimation were updated using sparse matrices to increase efficiency

- A new function to estimate gene-level p-values, based on Davies algortihm, was implemented

GALLO v1.4

- A new method to split the extra_info column from gff of Animal QTLdb was implemented. Therefore, the output of QTL annotation contains all the fields available in the extra_info column.

- The bug present was the end coordinates were bigger than the start coordinates were fixed. Now, GALLO automatically checks for these patterns and switches the coordinates.

- A new function to estimate gene-level p-values was implemented using a Weighted Z-score approach and Meta-analysis with LD correlation coefficients approaches

- A new function to estimate the number of independent markers using an adaptation of the simpleM method was implemented

- A new function to estimate the number of independent segments per chromosome based on the effective population size was implemented

- A new function to compute multi-trait test statistics for pleiotropic effects using summary statistics from association tests was implemented

- A new function to represent the association between two groups of variables in a dynamic network was implemented

- A new function to compute the centrality metrics for the nodes composing the network generated by the NetVis function was implemented


GALLO v1.3

- The bug resulting in the switch between the values in the column breed was fixed

GALLO v1.2

In this version the following updates were included:

- The bug resulting in the switch between the values in the columns Flank_markers and breed was fixed

- The proper citation for GALLO now can be obtained using the command citation("GALLO"")

GALLO v1.1

In this version the following updates were included:

- Inclusion of a match.arg function for the marker argument in the find_genes_qtls_around_markers function.

- The code to allow multithreading was updated in order to allow the user to choose one (1) thread as input.

- The inclusion of the argument horiz in the plot_qtl_info() function, which allow the user to choose if the legend will be plotted vertically or horizontally.

- Changes in the legend and plot area in the QTLentich_plot function in order to better address cases where the there is a large difference between the minimum and maximum number of QTLs annotated.

GALLO v0.0-99
