Files in aiminy/3UTR-Seq
An R package for processing and analyzing 3UTR,DOGs and 5UTR data
DESCRIPTION
NAMESPACE
R/AdjustBatch.R
R/CheckBatch.R
R/Compare2Pos.R
R/CompareToFeature.R
R/DEAnalysisAdjustByBatch.R
R/FilterTranscripts.R
R/GetIntergenicCount.R
R/InstallRequiredPackage.R
R/Loadlibrary.R
R/MatchTxs2Gene.R
R/NormalizedCount.R
R/NormalizedCountByDESeq.R
R/ProcessOutputFilesFrom3UTR.R
R/ProcessOutputFilesFrom3UTR_recounbt.R
R/ProcessOutputFilesFrom5Cases.R
R/ProcessOutputFilesFromDoGsOnly.R
R/ProcessTranscripts2.R
R/ReadGeneList.R
R/ReadInterestedGeneList.R
R/ReformatTxsGene.R
R/Sleuth.R
R/TestUseLongestTxsOfGene.R
R/Utility.R
R/convert.z.score.R
R/essize.R
README.md
ThreeUTR.Rproj
Three_UTR.md
Three_UTR_presentation.Rmd
Three_UTR_presentation.html
inst/bin/bash/BashCopyFromPegasus.sh
inst/bin/bash/BashRunConvertPeak2Bed.sh
inst/bin/bash/BashRunConvertPeak2Bed4Peng.sh
inst/bin/bash/Bash_12.sh
inst/bin/bash/Bash_run_submit_job.sh
inst/bin/bash/Bash_run_submit_job_2.sh
inst/bin/bash/Bash_run_submit_job_3.sh
inst/bin/bash/Bash_run_submit_job_4_sorted_bam.sh
inst/bin/bash/Bash_run_submit_job_4_sorted_bam_2.sh
inst/bin/bash/Check_if_DoGs_overlap_with_transcript.sh
inst/bin/bash/CombineFastqfile.sh
inst/bin/bash/ConvertBamtoBigwig.sh
inst/bin/bash/ConvertBed2Bw.sh
inst/bin/bash/ConvertBed2Bw_12_22_2015.sh
inst/bin/bash/ConvertBed2Bw_12_22_2015_2.sh
inst/bin/bash/GenerateBedFile4ChipSeqData.sh
inst/bin/bash/Make_Bin_4_genome.sh
inst/bin/bash/Process3UTR2.sh
inst/bin/bash/Process3UTR_3.sh
inst/bin/bash/Process3UTR_3_PJ.sh
inst/bin/bash/Process3UTR_3_rename.sh
inst/bin/bash/ProcessEnsemble.sh
inst/bin/bash/ProcessEnsemble2.sh
inst/bin/bash/Process_STAR_Bam_Use_cufflinks_with_anno.sh
inst/bin/bash/Process_UTR_7_28_2016.sh
inst/bin/bash/Run4STAR.sh
inst/bin/bash/RunAlignment.sh
inst/bin/bash/RunAlignment2.sh
inst/bin/bash/RunAlignment4SingleEnd.sh
inst/bin/bash/RunDEXSeq.sh
inst/bin/bash/RunDEXSeq_using_new_annotation.sh
inst/bin/bash/RunSTAR.sh
inst/bin/bash/RunSTAR_4_PJ.sh
inst/bin/bash/RunTopHat.sh
inst/bin/bash/Run_201348189-01_htseq_count.sh
inst/bin/bash/Run_201348189-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348189-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348189-01_tophat.sh
inst/bin/bash/Run_201348190-01_htseq_count.sh
inst/bin/bash/Run_201348190-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348190-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348190-01_tophat.sh
inst/bin/bash/Run_201348191-01_htseq_count.sh
inst/bin/bash/Run_201348191-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348191-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348191-01_tophat.sh
inst/bin/bash/Run_201348192-01_htseq_count.sh
inst/bin/bash/Run_201348192-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348192-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348192-01_tophat.sh
inst/bin/bash/Run_201348193-01_htseq_count.sh
inst/bin/bash/Run_201348193-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348193-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348193-01_tophat.sh
inst/bin/bash/Run_201348194-01_htseq_count.sh
inst/bin/bash/Run_201348194-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348194-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348194-01_tophat.sh
inst/bin/bash/Run_201348195-01_htseq_count.sh
inst/bin/bash/Run_201348195-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348195-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348195-01_tophat.sh
inst/bin/bash/Run_201348196-01_htseq_count.sh
inst/bin/bash/Run_201348196-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348196-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348196-01_tophat.sh
inst/bin/bash/Run_201348197-01_tophat.sh
inst/bin/bash/Run_201348198-01_tophat.sh
inst/bin/bash/Run_201348199-01_htseq_count.sh
inst/bin/bash/Run_201348199-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348199-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348199-01_tophat.sh
inst/bin/bash/Run_201348200-01_htseq_count.sh
inst/bin/bash/Run_201348200-01_htseq_count_4_sorted_bam.sh
inst/bin/bash/Run_201348200-01_htseq_count_4_sorted_bam_2.sh
inst/bin/bash/Run_201348200-01_tophat.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_bam2bed.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_count_plus_minus.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_2016-02-10-emp1_Dox_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_bam2bed.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_count_plus_minus.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_2016-02-10-emp1_WT_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_bam2bed.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_count_plus_minus.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_2016-02-10-emp2_Dox_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_bam2bed.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_count_plus_minus.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_2016-02-10-emp2_WT_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_ATP5A1_3UTR.sh
inst/bin/bash/Run_Aligned_3UTR.sh
inst/bin/bash/Run_Fq_24.sh
inst/bin/bash/Run_JunctionSeq.sh
inst/bin/bash/Run_JunctionSeq_2.sh
inst/bin/bash/Run_STAR_out_3UTR.sh
inst/bin/bash/Run_annovar.sh
inst/bin/bash/Run_check_2016-02-10-emp1_Dox.sh
inst/bin/bash/Run_check_2016-02-10-emp1_WT.sh
inst/bin/bash/Run_check_2016-02-10-emp2_Dox.sh
inst/bin/bash/Run_check_2016-02-10-emp2_WT.sh
inst/bin/bash/Run_check_hela_dox1.sh
inst/bin/bash/Run_check_hela_dox2.sh
inst/bin/bash/Run_check_hela_wt1.sh
inst/bin/bash/Run_check_hela_wt2.sh
inst/bin/bash/Run_hela_dox1_3UTR_bam2bed.sh
inst/bin/bash/Run_hela_dox1_3UTR_count_plus_minus.sh
inst/bin/bash/Run_hela_dox1_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_hela_dox1_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_hela_dox1_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_hela_dox2_3UTR_bam2bed.sh
inst/bin/bash/Run_hela_dox2_3UTR_count_plus_minus.sh
inst/bin/bash/Run_hela_dox2_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_hela_dox2_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_hela_dox2_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_hela_wt1_3UTR_bam2bed.sh
inst/bin/bash/Run_hela_wt1_3UTR_count_plus_minus.sh
inst/bin/bash/Run_hela_wt1_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_hela_wt1_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_hela_wt1_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_hela_wt2_3UTR_bam2bed.sh
inst/bin/bash/Run_hela_wt2_3UTR_count_plus_minus.sh
inst/bin/bash/Run_hela_wt2_3UTR_count_use_feature_count.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads_count.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads_count_4_Complementarity.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads_count_total.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads_count_using_coverageBed.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_reads_use_DoGs_only.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_DOG_use_total_reads.sh
inst/bin/bash/Run_hela_wt2_3UTR_get_read_counts_4_DoGs_only_general.sh
inst/bin/bash/Run_hela_wt2_3UTR_rm_exon_intron.sh
inst/bin/bash/Run_mutect.sh
inst/bin/bash/Run_process_bed_4_using_coverageBed.sh
inst/bin/bash/Run_process_hg19_gene.sh
inst/bin/bash/Run_process_hg19_gene_4_gene_plus_DoGs.sh
inst/bin/bash/Run_process_hg19_gene_to_SAF.sh
inst/bin/bash/Run_process_vcf.sh
inst/bin/bash/Run_strelka.sh
inst/bin/bash/Run_trimmed_2015-11-20-HET10_S9_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-HET8_S7_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-HET9_S8_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-KO10_S6_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-KO8_S2_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-KO9_S4_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-WT10_S5_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-WT8_S1_combined4f_tophat.sh
inst/bin/bash/Run_trimmed_2015-11-20-WT9_S3_combined4f_tophat.sh
inst/bin/bash/Run_use_gene_counts_in_Junction_Seq.sh
inst/bin/bash/ToCount.sh
inst/bin/bash/bam2bw.sh
inst/bin/bash/bash_SRA_submission.sh
inst/bin/bash/bash_SRA_submission_one_file.sh
inst/bin/bash/bash_SRA_submission_updated.sh
inst/bin/bash/bdg2bw.sh
inst/bin/bash/fetchChromSizes.sh
inst/bin/rscript/GetCountUseBash.r
inst/bin/rscript/analysisdog.r
inst/bin/rscript/convertbam2bed.r
man/AdjustBatch.Rd
man/CheckBatch.Rd
man/Compare2Pos.Rd
man/DEAnalysisAdjustByBatch.Rd
man/FilterTranscripts.Rd
man/InstallRequiredPackage.Rd
man/Loadlibrary.Rd
man/MatchTxs2Gene.R.Rd
man/NormalizedCount.Rd
man/ProcessOutputFilesFrom3UTR.Rd
man/ProcessOutputFilesFrom3UTR_recount.Rd
man/ProcessOutputFilesFrom5Cases.Rd
man/ProcessOutputFilesFromDoGsOnly.Rd
man/ProcessTranscript2.Rd
man/ReadGeneList.Rd
man/ReformatTxsGene.Rd
man/TestUseLongestTxsOfGene.Rd
man/annotatetranscript.Rd
man/convert.z.score.Rd
man/convertbam2bed.Rd
man/gaoidtransform.Rd
man/getcounts.Rd
man/getcountsfromMatchedbed.Rd
man/matchbed2annotation.Rd
man/norm_factors.Rd
man/parserAnnotationFile.Rd
man/parserreadfiles.Rd
