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Alignment.sh
Alignment.sh
 
 
BWA_samtools_flagstat.sh
BWA_samtools_flagstat.sh
 
 
BWA_samtools_sort.sh
BWA_samtools_sort.sh
 
 
Bioinformatics_Pipeline_2018 backup.sh
Bioinformatics_Pipeline_2018 backup.sh
 
 
Bioinformatics_Pipeline_2018.sh
Bioinformatics_Pipeline_2018.sh
 
 
CSAW_differential_binding_phipps.R
CSAW_differential_binding_phipps.R
 
 
CSAW_differential_binding_without_efficiencynorm_AP_09052018.R
CSAW_differential_binding_without_efficiencynorm_AP_09052018.R
 
 
DTbamcoveragetest.sh
DTbamcoveragetest.sh
 
 
Diffbind.R
Diffbind.R
 
 
Diffbind12m_default.R
Diffbind12m_default.R
 
 
K27me3 Nugen trim reports
K27me3 Nugen trim reports
 
 
K4me312mRmarkdown.R
K4me312mRmarkdown.R
 
 
K4me3_3m_TMMbin.R
K4me3_3m_TMMbin.R
 
 
MarkDuplicates.sh
MarkDuplicates.sh
 
 
README.md
README.md
 
 
Remove K27ac library barcodes.sh
Remove K27ac library barcodes.sh
 
 
Sai_convert_sam.sh
Sai_convert_sam.sh
 
 
Sam2bam_K4me3.sh
Sam2bam_K4me3.sh
 
 
Shuffle_splitmk2.sh
Shuffle_splitmk2.sh
 
 
Split_cutadapt_reports.sh
Split_cutadapt_reports.sh
 
 
TI_Nugen_trim_reports
TI_Nugen_trim_reports
 
 
VennDiagram.R
VennDiagram.R
 
 
bam_sort&index_deeptoolsQC.sh
bam_sort&index_deeptoolsQC.sh
 
 
bash_file_cat.sh
bash_file_cat.sh
 
 
bwa_aln_K4me3.sh
bwa_aln_K4me3.sh
 
 
createbigwig.sh
createbigwig.sh
 
 
csaw12m_TMMbin.R
csaw12m_TMMbin.R
 
 
csawH3K27me3_Lun_settings.R
csawH3K27me3_Lun_settings.R
 
 
csaw_TEMPLATE.R
csaw_TEMPLATE.R
 
 
csaw_example_script.rd
csaw_example_script.rd
 
 
csaw_remove_comp_bias_TMMb_15052018.R
csaw_remove_comp_bias_TMMb_15052018.R
 
 
download_NGS_Data.sh
download_NGS_Data.sh
 
 
fetchChromSizes.sh
fetchChromSizes.sh
 
 
merge_samtools_sort.sh
merge_samtools_sort.sh
 
 
sam2bam_K27ac.sh
sam2bam_K27ac.sh
 
 
sam2bam_TI.sh
sam2bam_TI.sh
 
 
samtools_index.sh
samtools_index.sh
 
 
samtools_sort.sh
samtools_sort.sh
 
 
samtools_sort_TI.sh
samtools_sort_TI.sh
 
 
shuffle_split.sh
shuffle_split.sh
 
 
test_nugen_adapter.sh
test_nugen_adapter.sh
 
 

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EpiAD

This repository is a culmination of files and code for analysis of ChIP-seq and other NGS data.

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Code dump for EpiAD project

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