Files in DISC-IISR/RNAseqAnalysis
A List of Relevent Functions RNA-seq data analysis
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/annotate.R
R/countT.R
R/filteR.R
R/fqcR.R
R/frqc.R
R/gene_exp.R
R/load_data.R
R/splice.R
RNAseqAnalysis.Rproj
dataset/SRR5253683_1.fastq.gz
dataset/SRR5253683_2.fastq.gz
dataset/SRR5253684_1.fastq.gz
dataset/SRR5253684_2.fastq.gz
dataset/SRR5253685_1.fastq.gz
dataset/SRR5253685_2.fastq.gz
dataset/SRR5253686_1.fastq.gz
dataset/SRR5253686_2.fastq.gz
dataset/SRR5253687_1.fastq.gz
dataset/SRR5253687_2.fastq.gz
dataset/SRR5253688_1.fastq.gz
dataset/SRR5253688_2.fastq.gz
dataset/SRR5253689_1.fastq.gz
dataset/SRR5253689_2.fastq.gz
dataset/SRR5253690_1.fastq.gz
dataset/SRR5253690_2.fastq.gz
dataset/SRR5253691_1.fastq.gz
dataset/SRR5253691_2.fastq.gz
dataset/SRR5253692_1.fastq.gz
dataset/SRR5253692_2.fastq.gz
dataset/SRR5253694_1.fastq.gz
dataset/SRR5253694_2.fastq.gz
dataset/SRR5253695_1.fastq.gz
dataset/SRR5253695_2.fastq.gz
dataset/SRR5253696_1.fastq.gz
dataset/SRR5253696_2.fastq.gz
dataset/SRR5253697_1.fastq.gz
dataset/SRR5253697_2.fastq.gz
extdata/SRR5253683.bam
extdata/SRR5253683.bam.bai
extdata/SRR5253684.bam
extdata/SRR5253684.bam.bai
extdata/SRR5253685.bam
extdata/SRR5253685.bam.bai
extdata/SRR5253686.bam
extdata/SRR5253686.bam.bai
extdata/SRR5253687.bam
extdata/SRR5253687.bam.bai
extdata/SRR5253688.bam
extdata/SRR5253688.bam.bai
extdata/SRR5253689.bam
extdata/SRR5253689.bam.bai
extdata/SRR5253690.bam
extdata/SRR5253690.bam.bai
extdata/SRR5253691.bam
extdata/SRR5253691.bam.bai
extdata/SRR5253692.bam
extdata/SRR5253692.bam.bai
extdata/SRR5253694.bam
extdata/SRR5253694.bam.bai
extdata/SRR5253695.bam
extdata/SRR5253695.bam.bai
extdata/SRR5253696.bam
extdata/SRR5253696.bam.bai
extdata/SRR5253697.bam
extdata/SRR5253697.bam.bai
man/annotate.Rd
man/countT.Rd
man/filteR.Rd
man/fqcR.Rd
man/frqc.Rd
man/gene_exp.Rd
man/import_dataset.Rd
man/splice.Rd
param/Makefile
param/Makefile_chipseq
param/Makefile_rnaseq
param/Makefile_varseq
param/annotate_peaks.param
param/annotate_vars.param
param/bibtex.bib
param/bowtiePE.param
param/bowtieSE.param
param/bwa.param
param/count_rangesets.param
param/filter_gatk.param
param/filter_sambcf.param
param/filter_vartools.param
param/gatk.param
param/gatk_run.sh
param/gsnap.param
param/hisat2.param
param/hisat2PE.param
param/macs2.param
param/macs2_noinput.param
param/rsubread.param
param/rundiff.param
param/sambcf.param
param/sambcf_run.sh
param/targets.txt
param/targetsPE.txt
param/targetsPE_chip.txt
param/targets_chip.txt
param/tophat.param
param/tophatV1.param
param/torque.tmpl
param/trim.param
param/trimPE.param
param/vartools.param
vignettes/A_plot_of_quality_by_base_position.jpeg
vignettes/Base_frequencies_by_position_in_sequence.jpeg
vignettes/Base_proportions_by_position_in_sequence.jpeg
vignettes/DEG_edgeR.jpeg
vignettes/Dendrogram_based_on_RPKM_values.jpeg
vignettes/Dendrogram_based_on_rlog_values.jpeg
vignettes/GC_content_by_position.jpeg
vignettes/GOslimbarplotBP.jpeg
vignettes/GOslimbarplotCC.jpeg
vignettes/GOslimbarplotMF.jpeg
vignettes/Introduction_to_RNASeq.R
vignettes/Introduction_to_RNASeq.Rmd
vignettes/Introduction_to_RNASeq.html
vignettes/K-L_terms_for_a_subset_of_top_k-mers.jpeg
vignettes/PCA_plot.jpeg
vignettes/StandardDeviation_basedon_RLtransformation.jpeg
vignettes/StandardDeviation_basedon_SLransformation.jpeg
vignettes/StandardDeviation_basedon_VSTransformation.jpeg
vignettes/average-quality-plot.jpeg
vignettes/biplot.jpeg
vignettes/box_plot.png
vignettes/count_matrix_based_on_regularized_log_transformation.jpeg
vignettes/count_matrix_based_on_shifted_logarithm_transformation.jpeg
vignettes/count_matrix_based_on_variance_stabilizing_transformation.jpeg
vignettes/counts_of_reads_across_groups.jpeg
vignettes/cycle-average-quality-plot.jpeg
vignettes/cycle-gc-plo.jpeg
vignettes/heatmap-reads.jpeg
vignettes/heatmap_of_distance_matrix.jpeg
vignettes/log2_fold_changes.jpeg
vignettes/log2_fold_changes_AfterNoiseRemoval.jpeg
vignettes/mystyles.css
vignettes/read-mean-dist.jpeg
vignettes/read-width-plot.jpeg
vignettes/read_density_based_on_log-cpm.png
vignettes/readfrequency.jpeg
vignettes/rpl-13_E003.png
vignettes/rpl-31_E009.png
vignettes/targets.txt
vignettes/targetsPE.txt
vignettes/tophat.param
vignettes/venndiagm_1_4.jpeg
vignettes/venndiagm_3_6.jpeg
