Files in pachterlab/zika
Tools for investigating RNA-Seq
.gitignore
.lintr
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
R/bootstrap.R
R/gene_analysis.R
R/hexamers.R
R/import.R
R/kallisto.R
R/likelihood.R
R/matrix.R
R/measurement_error.R
R/misc.R
R/model.R
R/plots.R
R/read_write.R
R/shiny.R
R/sleuth.R
R/units.R
README.md
analyze_data.R
inst/doc/intro.html
inst/scripts/gen_hexamers.sh
inst/scripts/hexamers.py
kallisto_output/SRR3191542/abundance.h5
kallisto_output/SRR3191542/abundance.tsv
kallisto_output/SRR3191542/run_info.json
kallisto_output/SRR3191543/abundance.h5
kallisto_output/SRR3191543/abundance.tsv
kallisto_output/SRR3191543/run_info.json
kallisto_output/SRR3191544/abundance.h5
kallisto_output/SRR3191544/abundance.tsv
kallisto_output/SRR3191544/run_info.json
kallisto_output/SRR3191545/abundance.h5
kallisto_output/SRR3191545/abundance.tsv
kallisto_output/SRR3191545/run_info.json
kallisto_output/SRR3194428/abundance.h5
kallisto_output/SRR3194428/abundance.tsv
kallisto_output/SRR3194428/run_info.json
kallisto_output/SRR3194429/abundance.h5
kallisto_output/SRR3194429/abundance.tsv
kallisto_output/SRR3194429/run_info.json
kallisto_output/SRR3194430/abundance.h5
kallisto_output/SRR3194430/abundance.tsv
kallisto_output/SRR3194430/run_info.json
kallisto_output/SRR3194431/abundance.h5
kallisto_output/SRR3194431/abundance.tsv
kallisto_output/SRR3194431/run_info.json
man/basic_filter.Rd
man/design_matrix.Rd
man/get_bootstraps.Rd
man/get_col.Rd
man/kallisto_table.Rd
man/models.Rd
man/norm_factors.Rd
man/plot_bootstrap.Rd
man/plot_fld.kallisto.Rd
man/plot_fld.sleuth.Rd
man/plot_group_density.Rd
man/plot_loadings.Rd
man/plot_ma.Rd
man/plot_mean_var.Rd
man/plot_pc_variance.Rd
man/plot_pca.Rd
man/plot_qq.Rd
man/plot_sample_density.Rd
man/plot_sample_heatmap.Rd
man/plot_scatter.Rd
man/plot_transcript_heatmap.Rd
man/plot_vars.Rd
man/plot_volcano.Rd
man/print.sleuth_model.Rd
man/read_kallisto.Rd
man/read_kallisto_h5.Rd
man/read_kallisto_tsv.Rd
man/sleuth_fit.Rd
man/sleuth_gene_table.Rd
man/sleuth_live.Rd
man/sleuth_live_settings.Rd
man/sleuth_lrt.Rd
man/sleuth_prep.Rd
man/sleuth_results.Rd
man/sleuth_to_matrix.Rd
man/sleuth_wt.Rd
man/transcripts_from_gene.Rd
tests/testthat.R
tests/testthat/ellahi/README.md
tests/testthat/ellahi/SRR1811834/kallisto/abundance.h5
tests/testthat/ellahi/SRR1812754/kallisto/abundance.h5
tests/testthat/ellahi/SRR1812759/kallisto/abundance.h5
tests/testthat/ellahi/SRR1812760/kallisto/abundance.h5
tests/testthat/ellahi/SRR1812767/kallisto/abundance.h5
tests/testthat/ellahi/SRR1812768/kallisto/abundance.h5
tests/testthat/ellahi/study_design.txt
tests/testthat/helper-setup.R
tests/testthat/small_test_data/abundance.h5
tests/testthat/small_test_data/abundance.tsv
tests/testthat/small_test_data/run_info.json
tests/testthat/test-lintr.R
tests/testthat/test-prep.R
tests/testthat/test-read.R
vignettes/figure/unnamed-chunk-1-1.png
vignettes/figure/unnamed-chunk-1-2.png
vignettes/intro.Rmd
zikadesignmatrix.txt
