Bioinformatics

Workflows and scripts related to Bioinformatics

Name		Name	Last commit message	Last commit date
ANNOVAR-2-REDCap		ANNOVAR-2-REDCap
Benchmarking		Benchmarking
ChIPseeker_profile_plots		ChIPseeker_profile_plots
DiffBind		DiffBind
DiffBind_scripts_reports		DiffBind_scripts_reports
HITS-CLIP_pipeline		HITS-CLIP_pipeline
HOMER_mergePeaks_pipeline		HOMER_mergePeaks_pipeline
HOMER_motif_analysis		HOMER_motif_analysis
HiC-Bench-utils		HiC-Bench-utils
IGV-snapshot-wrapper		IGV-snapshot-wrapper
MACS2-params-testing		MACS2-params-testing
MuTect2-filter-testing		MuTect2-filter-testing
MuTect2-variant-aggregation		MuTect2-variant-aggregation
NYGC_download		NYGC_download
Oncomine		Oncomine
Oncomine_NGS50_overlap		Oncomine_NGS50_overlap
PAR-CLIP_pipeline		PAR-CLIP_pipeline
Python_scripts		Python_scripts
QualityControl		QualityControl
SeraCare_variant_analysis		SeraCare_variant_analysis
SuperEnhancer_calling		SuperEnhancer_calling
UCSC_custom_tracks		UCSC_custom_tracks
anaconda		anaconda
annotate_peaks_ChIPpeakAnno		annotate_peaks_ChIPpeakAnno
bedtools_coverage_chrY		bedtools_coverage_chrY
benchmarking_GetBaseCountsMultiSample		benchmarking_GetBaseCountsMultiSample
bowtie2_alignment_indexing		bowtie2_alignment_indexing
clustering_heatmaps		clustering_heatmaps
code		code
data		data
fastq_filter_by_region		fastq_filter_by_region
fusions-Delly2		fusions-Delly2
gene_plots		gene_plots
genomic_signatures		genomic_signatures
get_TSS_regions_Gencode_Ensembl		get_TSS_regions_Gencode_Ensembl
iGenomes		iGenomes
misc_workflow		misc_workflow
mutational_signatures-deconstructSigs		mutational_signatures-deconstructSigs
peak_overlap_multi_report		peak_overlap_multi_report
peaks-per-sample_HiCBench-MACS2_report		peaks-per-sample_HiCBench-MACS2_report
peaks_annotation_summaries_ChIPSeeker		peaks_annotation_summaries_ChIPSeeker
peaks_vs_alignments_per_sample_plots		peaks_vs_alignments_per_sample_plots
pipeline-peaks-report		pipeline-peaks-report
python_read_heredoc		python_read_heredoc
reverse_compliment-shiny		reverse_compliment-shiny
sample-data		sample-data
scripts		scripts
signatures_aggregate		signatures_aggregate
survival		survival
tcga-tmb-analysis		tcga-tmb-analysis
.gitignore		.gitignore
MACS1_BigWig_workflow.sh		MACS1_BigWig_workflow.sh
README.md		README.md
bed_chrom_split.py		bed_chrom_split.py
bed_dir_barplot.R		bed_dir_barplot.R
bowtie2_MACS1_bedGraph_workflow2.sh		bowtie2_MACS1_bedGraph_workflow2.sh
clusterProfiler_DiffBind_GO_pipeline.R		clusterProfiler_DiffBind_GO_pipeline.R
enable_sns_setx.sh		enable_sns_setx.sh
find_missing_file.py		find_missing_file.py
find_missing_files.py		find_missing_files.py
find_missing_samples.py		find_missing_samples.py
phoenix_cluster_HOMER_example.md		phoenix_cluster_HOMER_example.md
references.bib		references.bib
run_MuTect2_split.sh		run_MuTect2_split.sh
run_gtools_make_matrices.py		run_gtools_make_matrices.py
sort-bed.sh		sort-bed.sh
toolbox.py		toolbox.py
transfer_BaseSpace_to_NGS_sequencer_dir.sh		transfer_BaseSpace_to_NGS_sequencer_dir.sh

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