BIRD_v1.1.1

Starting from this version, the prebuilt prediction models will not be included in this repo. Users can download the required models from https://github.com/WeiqiangZhou/BIRD-model.

Important updates:

1. The quantile normalization function is updated to a more robust version (significantly boost prediction performance when there is a large number of tied values in the input data, e.g., single-cell RNA-seq data).

2. Input data matching (gene id matching) is now included in the BIRD_predict program. Users don't have to prepare the input data matrix with the legacy R script match_input_matrix.r. Please read the How to use (for RNA-seq and single-cell RNA-seq) section for details.

3. The predicted values are now bounded from 0 to 14. Users can use the -u option to change the upper bound when using their own prediction model. Users can also use -l option to perform prediction using the locus-level model rather than using the full model. This is useful when you build your own prediction model but you are not sure if the cluster-level model works or not.

Minor updates:

1. An option is added for outputting wig files with log-transformed values.

2. Add RNA-seq data and script for calculating training test distance.

BIRD_v1.1

Add more options to the prediction function.
Rename ref_gene.txt as gene_name.txt

BIRD v1.0.3

Add preparing FPKM data matrix input function!

BIRD v1.0.2

BIRD v1.0
BIRD is a software to predict DNase I hypersensitivity using gene expression data.
Supports Linux/Unix system.
BIRD_bash.sh added for large dataset.

BIRD v1.0.1
BIRD model updated with model averaging.

BIRD v1.0.2
Now supports RNA-seq data!