chambm/customProDB
Generate customized protein databases from NGS data for proteomics search

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Generate customized protein databases from NGS data for proteomics search

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/Bed2Range.R R/Ensembl.utils.R R/InputVcf.R R/JunctionType.R R/Multiple_VCF.R R/OutputNovelJun.R R/OutputVarprocodingseq.R R/OutputVarproseq.R R/OutputVarproseq_single.R R/Outputaberrant.R R/Outputproseq.R R/OutputsharedPro.R R/Positionincoding.R R/PrepareAnnotationEnsembl.R R/PrepareAnnotationGCF.R R/PrepareAnnotationRefseq.R R/SharedJunc.R R/Varlocation.R R/aaVariation.R R/calculateRPKM.R R/customProDB.R R/easyRun.R R/easyRun_mul.R R/getVariantAnnotation.R R/utils.R README.md
codecov.yml
customProDB.Rproj
inst/CITATION
inst/extdata/bams/test1_sort.bam
inst/extdata/bams/test1_sort.bam.bai
inst/extdata/bams/test2_sort.bam
inst/extdata/bams/test2_sort.bam.bai
inst/extdata/bams/test3_sort.bam
inst/extdata/bams/test3_sort.bam.bai
inst/extdata/beds/junctions1.bed
inst/extdata/beds/junctions2.bed
inst/extdata/beds/junctions3.bed
inst/extdata/cache/cfamiliaris_gene_ensembl_87/coding.rds
inst/extdata/cache/cfamiliaris_gene_ensembl_87/exon.rds
inst/extdata/cache/cfamiliaris_gene_ensembl_87/idstab.rds
inst/extdata/cache/cfamiliaris_gene_ensembl_87/proteinseq.rds
inst/extdata/cache/cfamiliaris_gene_ensembl_87/tr.rds
inst/extdata/cache/cfamiliaris_gene_ensembl_87/txdb.sqlite
inst/extdata/cache/hg19/cosmic.rds
inst/extdata/cache/hg19/refGene.rds
inst/extdata/cache/hg19/reflink.rds
inst/extdata/cache/hg19/snp141/snpCodingTab.rds
inst/extdata/cache/hg19/snp146/snpCodingTab.rds
inst/extdata/cache/hg19/txdb.sqlite
inst/extdata/cache/hg38/refGene.rds
inst/extdata/cache/hg38/reflink.rds
inst/extdata/cache/hg38/snp147/snpCodingTab.rds
inst/extdata/cache/hg38/txdb.sqlite
inst/extdata/cache/hsapiens_gene_ensembl_82/coding.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/exon.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/idstab.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/proteinseq.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/snp146/dbsnpinCoding.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/tr.rds
inst/extdata/cache/hsapiens_gene_ensembl_82/txdb.sqlite
inst/extdata/cache/hsapiens_gene_ensembl_87/coding.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/cosmic.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/exon.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/idstab.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/proteinseq.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/snp146/dbsnpinCoding.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/tr.rds
inst/extdata/cache/hsapiens_gene_ensembl_87/txdb.sqlite
inst/extdata/cache/mm10/refGene.rds
inst/extdata/cache/mm10/reflink.rds
inst/extdata/cache/mm10/snp142/snpCodingTab.rds
inst/extdata/cache/mm10/txdb.sqlite
inst/extdata/cache/mmusculus_gene_ensembl_87/coding.rds
inst/extdata/cache/mmusculus_gene_ensembl_87/exon.rds
inst/extdata/cache/mmusculus_gene_ensembl_87/idstab.rds
inst/extdata/cache/mmusculus_gene_ensembl_87/proteinseq.rds
inst/extdata/cache/mmusculus_gene_ensembl_87/tr.rds
inst/extdata/cache/mmusculus_gene_ensembl_87/txdb.sqlite
inst/extdata/cache/scerevisiae_gene_ensembl_87/coding.rds
inst/extdata/cache/scerevisiae_gene_ensembl_87/exon.rds
inst/extdata/cache/scerevisiae_gene_ensembl_87/idstab.rds
inst/extdata/cache/scerevisiae_gene_ensembl_87/proteinseq.rds
inst/extdata/cache/scerevisiae_gene_ensembl_87/tr.rds
inst/extdata/cache/scerevisiae_gene_ensembl_87/txdb.sqlite
inst/extdata/gcf/test_NIST_Tur_tru_v1_assembly_report.txt
inst/extdata/gcf/test_NIST_Tur_tru_v1_cds_from_genomic.fna
inst/extdata/gcf/test_NIST_Tur_tru_v1_genomic.gff
inst/extdata/gcf/test_NIST_Tur_tru_v1_translated_cds.faa
inst/extdata/hg19/hg19_coding.fasta
inst/extdata/hg19/hg19_protein.fasta
inst/extdata/hg38/hg38_coding.fasta
inst/extdata/hg38/hg38_protein.fasta
inst/extdata/mm10/mm10_coding.fasta
inst/extdata/mm10/mm10_protein.fasta
inst/extdata/mmusculus_gene_ensembl_87/dbsnpinCoding.RData
inst/extdata/mmusculus_gene_ensembl_87/exon_anno.RData
inst/extdata/mmusculus_gene_ensembl_87/ids.RData
inst/extdata/mmusculus_gene_ensembl_87/procodingseq.RData
inst/extdata/mmusculus_gene_ensembl_87/proseq.RData
inst/extdata/mmusculus_gene_ensembl_87/test.bam
inst/extdata/mmusculus_gene_ensembl_87/test.bam.bai
inst/extdata/mmusculus_gene_ensembl_87/test.vcf
inst/extdata/refseq/cosmic.RData
inst/extdata/refseq/dbsnpinCoding.RData
inst/extdata/refseq/exon_anno.RData
inst/extdata/refseq/ids.RData
inst/extdata/refseq/procodingseq.RData
inst/extdata/refseq/proseq.RData
inst/extdata/refseq/splicemax.RData
inst/extdata/refseq/txdb.sqlite
inst/extdata/test_mul.vcf
inst/extdata/tmp/test_indel.fasta
inst/extdata/tmp/test_junc.fasta
inst/extdata/tmp/test_rpkm.fasta
inst/extdata/tmp/test_snv.fasta
inst/extdata/tmp/test_snv.tab
inst/extdata/vcfs/test1.vcf
inst/extdata/vcfs/test2.vcf
inst/extdata/vcfs/test3.vcf
man/Bed2Range.Rd man/InputVcf.Rd man/JunctionType.Rd man/Multiple_VCF.Rd man/OutputNovelJun.Rd man/OutputVarprocodingseq.Rd man/OutputVarproseq.Rd man/OutputVarproseq_single.Rd man/Outputaberrant.Rd man/Outputproseq.Rd man/OutputsharedPro.Rd man/Positionincoding.Rd man/PrepareAnnotationEnsembl.Rd man/PrepareAnnotationGCF.Rd man/PrepareAnnotationRefseq.Rd man/SharedJunc.Rd man/Varlocation.Rd man/aaVariation.Rd man/calculateRPKM.Rd man/current_script_file.Rd man/customProDB.Rd man/easyRun.Rd man/easyRun_mul.Rd man/expect_equal_to_reference.Rd man/fastComplement.Rd man/getCodingFastaUrlFromUCSC.Rd man/getProteinFastaUrlFromUCSC.Rd man/getVariantAnnotation.Rd man/read_or_update_local_cache.Rd man/variantType.Rd tests/testthat.R
tests/testthat/cosmic_hg19.rds
tests/testthat/cosmic_hsapiens_gene_ensembl_87.rds
tests/testthat/dbsnpinCoding_hg19_snp141.rds
tests/testthat/dbsnpinCoding_hg19_snp146.rds
tests/testthat/dbsnpinCoding_hg38_snp147.rds
tests/testthat/dbsnpinCoding_hsapiens_gene_ensembl_82_snp146.rds
tests/testthat/dbsnpinCoding_hsapiens_gene_ensembl_87_snp146.rds
tests/testthat/dbsnpinCoding_mm10_snp142.rds
tests/testthat/exon_Tur_tru_v1.rds
tests/testthat/exon_cfamiliaris_gene_ensembl_87.rds
tests/testthat/exon_hg19.rds
tests/testthat/exon_hg38.rds
tests/testthat/exon_hsapiens_gene_ensembl_82.rds
tests/testthat/exon_hsapiens_gene_ensembl_87.rds
tests/testthat/exon_mm10.rds
tests/testthat/exon_mmusculus_gene_ensembl_87.rds
tests/testthat/exon_scerevisiae_gene_ensembl_87.rds
tests/testthat/hg19_jun_anno.rds
tests/testthat/hg19_junpep.rds
tests/testthat/hg19_junpepcoding.rds
tests/testthat/ids_Tur_tru_v1.rds
tests/testthat/ids_cfamiliaris_gene_ensembl_87.rds
tests/testthat/ids_hg19.rds
tests/testthat/ids_hg38.rds
tests/testthat/ids_hsapiens_gene_ensembl_82.rds
tests/testthat/ids_hsapiens_gene_ensembl_87.rds
tests/testthat/ids_mm10.rds
tests/testthat/ids_mmusculus_gene_ensembl_87.rds
tests/testthat/ids_scerevisiae_gene_ensembl_87.rds
tests/testthat/procodingseq_Tur_tru_v1.rds
tests/testthat/procodingseq_cfamiliaris_gene_ensembl_87.rds
tests/testthat/procodingseq_hg19.rds
tests/testthat/procodingseq_hg38.rds
tests/testthat/procodingseq_hsapiens_gene_ensembl_82.rds
tests/testthat/procodingseq_hsapiens_gene_ensembl_87.rds
tests/testthat/procodingseq_mm10.rds
tests/testthat/procodingseq_mmusculus_gene_ensembl_87.rds
tests/testthat/procodingseq_scerevisiae_gene_ensembl_87.rds
tests/testthat/proseq_Tur_tru_v1.rds
tests/testthat/proseq_cfamiliaris_gene_ensembl_87.rds
tests/testthat/proseq_hg19.rds
tests/testthat/proseq_hg38.rds
tests/testthat/proseq_hsapiens_gene_ensembl_82.rds
tests/testthat/proseq_hsapiens_gene_ensembl_87.rds
tests/testthat/proseq_mm10.rds
tests/testthat/proseq_mmusculus_gene_ensembl_87.rds
tests/testthat/proseq_scerevisiae_gene_ensembl_87.rds
tests/testthat/test-OutputNovelJun.R tests/testthat/test-OutputVarprocodingseq.R tests/testthat/test-OutputVarproseq.R tests/testthat/test-Outputproseq.R tests/testthat/test-PrepareAnnotationEnsembl.R tests/testthat/test-PrepareAnnotationGCF.R tests/testthat/test-PrepareAnnotationRefseq.R
tests/testthat/test-easyRun-mmusculus_gene_ensembl_87_rpkm.fasta.rds
tests/testthat/test-easyRun-test_indel.fasta.rds
tests/testthat/test-easyRun-test_junc.fasta.rds
tests/testthat/test-easyRun-test_snv.fasta.rds
tests/testthat/test-easyRun-test_snv_dbsnp.fasta.rds
tests/testthat/test-easyRun.R tests/testthat/test-getVariantAnnotation.R
tests/testthat/test1-hg19-aaVariation.rds
tests/testthat/test1-hg19-indelprocoding.rds
tests/testthat/test1-hg19-indelproseq.rds
tests/testthat/test1-hg19-snvprocoding.rds
tests/testthat/test1-hg19-snvproseq.rds
tests/testthat/test_rpkm0.fasta.rds
tests/testthat/test_rpkm1000.fasta.rds
tests/testthat/test_snv.fasta.rds
tests/testthat/test_snv.fasta_snvprocodingseq.rds
tests/testthat/test_snv.fasta_snvproseq.rds
vignettes/customProDB.Rnw
chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.

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