Files in foreverycc/AlleleSNP_Package
Identify allele-specific effects of SNPs through sequencing data
.Rbuildignore
.gitignore
AlleleSNP.Rproj
DESCRIPTION
NAMESPACE
R/F1.1-get_ldsnp_info.R
R/F1.2-get_snp_annotation.R
R/F2.1-get_alleleDist_info.R
R/F2.2-get_peak_info.R
R/F2.3-get_vcf_info.R
R/F2.4-get_cnv_info.R
R/F2.4.1-get_loci_cnv_byEthic.R
R/F2.4.1.1-indexSNP_class.R
R/F2.5-get_cnv_info_encode.R
R/F3-get_ase_snp.R
R/M1-get_assnp.R
R/M2-get_assnp_local.R
R/M3-get_assnp_encode.R
R/T1-toolbox.R
README.md
README.md~
data/encode_cnv_gr_list.rda
inst/extdata/input_snps/input_snp_example1.csv
inst/extdata/input_snps/input_snp_example2.csv
inst/extdata/sample/A549/bam_files/A549_H3K27ac.bam
inst/extdata/sample/A549/bam_files/A549_H3K27ac.bam.bai
inst/extdata/sample/A549/bam_files/A549_H3K4me1.bam
inst/extdata/sample/A549/bam_files/A549_H3K4me1.bam.bai
inst/extdata/sample/A549/bam_files/A549_H3K4me3.bam
inst/extdata/sample/A549/bam_files/A549_H3K4me3.bam.bai
inst/extdata/sample/A549/bam_files/A549_H3K9ac.bam
inst/extdata/sample/A549/bam_files/A549_H3K9ac.bam.bai
inst/extdata/sample/A549/bam_files/A549_PolII.bam
inst/extdata/sample/A549/bam_files/A549_PolII.bam.bai
inst/extdata/sample/A549/peak_files/A549_H3K27ac_peaks.bed
inst/extdata/sample/A549/peak_files/A549_H3K4me1_peaks.bed
inst/extdata/sample/A549/peak_files/A549_H3K4me3_peaks.bed
inst/extdata/sample/A549/peak_files/A549_H3K9ac_peaks.bed
inst/extdata/sample/A549/peak_files/A549_PolII_peaks.bed
inst/extdata/sample/A549/vcf_files/A549_ChIPseq_GATK.vcf
inst/extdata/sample/A549/vcf_files/A549_ChIPseq_Samtools.vcf
inst/extdata/sample/A549/vcf_files/A549_WGS_GATK.vcf
man/AlleleSNP_Introduction.pdf
tests/test.R
