All modules for which code is available
- process_align_bowtie
- process_align_bwa
- process_align_bwa_mem
- process_biobambam
- process_bs_seeker_aligner
- process_bs_seeker_filter
- process_bs_seeker_index
- process_bsgenome
- process_chipseq
- process_damidseq
- process_genome
- process_hic
- process_iNPS
- process_macs2
- process_mnaseseq
- process_rnaseq
- process_trim_galore
- tests.test_pipeline_chipseq
- tests.test_pipeline_genome
- tests.test_pipeline_idamidseq
- tests.test_pipeline_mnaseseq
- tests.test_pipeline_rnaseq
- tests.test_pipeline_tb
- tests.test_toolchains
- tool.aligner_utils
- tool.bam_utils
- tool.biobambam_filter
- tool.bowtie_aligner
- tool.bowtie_indexer
- tool.bs_seeker_aligner
- tool.bs_seeker_filter
- tool.bs_seeker_indexer
- tool.bwa_aligner
- tool.bwa_indexer
- tool.bwa_mem_aligner
- tool.common
- tool.fastq_splitter
- tool.fastq_utils
- tool.fastqreader
- tool.forge_bsgenome
- tool.gem_indexer
- tool.idear
- tool.inps
- tool.kallisto_indexer
- tool.kallisto_quant
- tool.macs2
- tool.tb_bin
- tool.tb_filter
- tool.tb_full_mapping
- tool.tb_generate_tads
- tool.tb_model
- tool.tb_normalize
- tool.tb_parse_mapping
- tool.tb_save_hdf5_matrix
- tool.tb_segment
- tool.trimgalore
- tool.validate_fastqc