Files in zhezhangsh/Rnaseq
.DS_Store
DESCRIPTION
NAMESPACE
R/.Rapp.history
R/Alignment.r
R/AnalyzeJunction.r
R/CalculateCNV.R
R/ConvertSam2Bam.R
R/CountRead.R
R/LoadBam.R
R/LoadGa.R
R/LoadHTseq.R
R/MapExon2Gene.R
R/NormalizeRNAseq.R
R/PlotLogScatter.R
R/ProcessRnaseq.R
R/RunStar.R
README.md
Rnaseq.Rproj
examples/.DS_Store
examples/AnalyzeRNAseqSample/AnalyzeRNAseqSample.Rmd
examples/AnalyzeRNAseqSample/AnalyzeRNAseqSample.yml
examples/AnalyzeRNAseqSample/input/anno_entrez.rds
examples/AnalyzeRNAseqSample/input/count_entrez.rds
examples/AnalyzeRNAseqSample/input/gene_length_entrez.rds
examples/AnalyzeRNAseqSample/input/id_by_chr.rds
examples/AnalyzeRNAseqSample/input/sample.rds
examples/AnalyzeRNAseqSample/output/AnalyzeRNAseqSample.Rmd
examples/AnalyzeRNAseqSample/output/AnalyzeRNAseqSample.md
examples/AnalyzeRNAseqSample/output/AnalyzeRNAseqSample.yml
examples/AnalyzeRNAseqSample/output/PCA_CdLS.pdf
examples/AnalyzeRNAseqSample/output/PCA_Clone.pdf
examples/AnalyzeRNAseqSample/output/PCA_Gender.pdf
examples/AnalyzeRNAseqSample/output/PCA_Subject.pdf
examples/AnalyzeRNAseqSample/output/figure/clustering-1.png
examples/AnalyzeRNAseqSample/output/figure/gender_prediction-1.png
examples/AnalyzeRNAseqSample/output/figure/gene_count_pct-1.png
examples/AnalyzeRNAseqSample/output/figure/pca-1.png
examples/AnalyzeRNAseqSample/output/figure/pca_fields-1.png
examples/AnalyzeRNAseqSample/output/figure/read_count_dist-1.png
examples/AnalyzeRNAseqSample/output/fpkm.rds
examples/AnalyzeRNAseqSample/output/index.html
examples/AnalyzeRNAseqSample/output/output.zip
examples/AnalyzeRNAseqSample/output/sample_summary.html
examples/AnalyzeRNAseqSample/output/sample_summary_files/datatables-1.10.7/jquery.dataTables.min.js
examples/AnalyzeRNAseqSample/output/sample_summary_files/datatables-binding-0.1.40/datatables.js
examples/AnalyzeRNAseqSample/output/sample_summary_files/datatables-default-1.10.7/dataTables.extra.css
examples/AnalyzeRNAseqSample/output/sample_summary_files/datatables-default-1.10.7/jquery.dataTables.min.css
examples/AnalyzeRNAseqSample/output/sample_summary_files/htmlwidgets-0.5.2/htmlwidgets.js
examples/AnalyzeRNAseqSample/output/sample_summary_files/jquery-1.11.1/LICENSE.txt
examples/AnalyzeRNAseqSample/output/sample_summary_files/jquery-1.11.1/jquery.min.js
examples/AnalyzeRNAseqSample/output/sample_summary_files/nouislider-7.0.10/jquery.nouislider.min.css
examples/AnalyzeRNAseqSample/output/sample_summary_files/nouislider-7.0.10/jquery.nouislider.min.js
examples/AnalyzeRNAseqSample/output/sample_summary_files/selectize-0.12.0/selectize.bootstrap3.css
examples/AnalyzeRNAseqSample/output/sample_summary_files/selectize-0.12.0/selectize.min.js
examples/LoadBam/LoadBam.yml
examples/LoadBam/LoadBamScript.r
examples/LoadBam/LoadBamScript.yml
examples/LoadBam/development/LoadBam.r
examples/LoadBam/development/LoadBam.sh
examples/LoadBam/development/LoadBam.yml
examples/LoadBam/development/LoadBamSet.yml
examples/LoadBam/development/LoadGa.yaml
examples/LoadBam/development/LoadGaFromYaml.r
examples/LoadBam/development/load_bams.r
examples/LoadBam/development/qsub.sh
examples/ProcessRnaseq/ProcessRnaseq.yaml
examples/ProcessRnaseq/processing_data/adjust_batch/adjust_batch.r
examples/ProcessRnaseq/processing_data/adjust_batch/adjust_batch.sh
examples/ProcessRnaseq/processing_data/adjust_batch/adjust_batch.yaml
examples/ProcessRnaseq/processing_data/identify_outlier/identify_outlier.r
examples/ProcessRnaseq/processing_data/identify_outlier/identify_outlier.sh
examples/ProcessRnaseq/processing_data/identify_outlier/identify_outlier.yaml
examples/ProcessRnaseq/processing_data/load_bam/ND410-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND410-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND410-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND410-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND410-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND410-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND410-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND410-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND410-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND422-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND422-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND422-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND422-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND422-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND422-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND422-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND422-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND422-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND426-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND426-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND426-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND426-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND426-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND426-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/ND430-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/ND430-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/ND430-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1077-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE1169-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE985-B/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE985-B/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE985-B/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE985-M/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE985-M/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE985-M/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/SLE985-T/LoadBam.r
examples/ProcessRnaseq/processing_data/load_bam/SLE985-T/LoadBam.sh
examples/ProcessRnaseq/processing_data/load_bam/SLE985-T/LoadBam.yml
examples/ProcessRnaseq/processing_data/load_bam/count.r
examples/ProcessRnaseq/processing_data/load_bam/file_count.rds
examples/ProcessRnaseq/processing_data/load_bam/load_bam.sh
examples/ProcessRnaseq/processing_data/load_bam/qsub.sh
examples/ProcessRnaseq/processing_data/pass_1/RunStar.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND410-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND410-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND410-T.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND422-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND422-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND422-T.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND426-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND426-T.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_ND430-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1077-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1077-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1077-T.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1169-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1169-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE1169-T.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE985-B.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE985-M.sh
examples/ProcessRnaseq/processing_data/pass_1/qsub/STAR_SLE985-T.sh
examples/ProcessRnaseq/processing_data/pass_1/script/combined_junction.r
examples/ProcessRnaseq/processing_data/pass_1/script/delete_sam.sh
examples/ProcessRnaseq/processing_data/pass_2/RunStar.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND410-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND410-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND410-T.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND422-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND422-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND422-T.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND426-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND426-T.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_ND430-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1077-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1077-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1077-T.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1169-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1169-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE1169-T.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE985-B.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE985-M.sh
examples/ProcessRnaseq/processing_data/pass_2/qsub/STAR_SLE985-T.sh
examples/ProcessRnaseq/processing_data/pass_2/script/combined_junction.r
examples/ProcessRnaseq/processing_data/pass_2/script/delete_sam.sh
examples/ProcessRnaseq/processing_data/rnaseq_sample/rnaseq_sample.r
examples/ProcessRnaseq/processing_data/rnaseq_sample/rnaseq_sample.sh
examples/ProcessRnaseq/processing_data/rnaseq_sample/rnaseq_sample.yaml
examples/ProcessRnaseq/processing_data/summarize_star/summarize_star.r
examples/ProcessRnaseq/processing_data/summarize_star/summarize_star.sh
examples/ProcessRnaseq/processing_data/summarize_star/summarize_star.yaml
examples/RunStar/RunStar.yml
examples/RunStar/development/RunStar.r
examples/RunStar/development/StarPerSample.yaml
examples/RunStar/development/StarPerSample_1pass.yaml
examples/Sam2Bam.yaml
examples/SummarizeStar/SummarizeStar.Rmd
examples/SummarizeStar/SummarizeStar.yml
examples/SummarizeStar/output/SummarizeStar.Rmd
examples/SummarizeStar/output/SummarizeStar.md
examples/SummarizeStar/output/SummarizeStar.yml
examples/SummarizeStar/output/figure/alignment_rate-1.pdf
examples/SummarizeStar/output/figure/alignment_rate-1.png
examples/SummarizeStar/output/figure/mismatch_indel-1.pdf
examples/SummarizeStar/output/figure/mismatch_indel-1.png
examples/SummarizeStar/output/figure/splice_noncanonical-1.pdf
examples/SummarizeStar/output/figure/splice_noncanonical-1.png
examples/SummarizeStar/output/figure/unique_multiple-1.pdf
examples/SummarizeStar/output/figure/unique_multiple-1.png
examples/SummarizeStar/output/figure/unmapped_outlier-1.pdf
examples/SummarizeStar/output/figure/unmapped_outlier-1.png
examples/SummarizeStar/output/index.html
examples/SummarizeStar/output/output.zip
export_functions.r
