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Bioinformatics analysis scripts, workflows, general code examples

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523 Commits
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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Bioinformatics

Workflows and scripts related to Bioinformatics

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Bioinformatics analysis scripts, workflows, general code examples

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