MACS
MACS -- Model-based Analysis of ChIP-Seq
파일 탐색기
최종 버전 다운로드 (.zip)- bug_report.md
- feature_request.md
- general_question.md
- windows_issues.md
- build-and-test-MACS3-macos.yml
- build-and-test-MACS3-non-x64-others.yml
- build-and-test-MACS3-non-x64.yml
- build-and-test-MACS3-website.yml
- build-and-test-MACS3-x64.yml
- macs-version-benchmark.yml
- publish-to-gh-with-sphinx.yml
- publish-to-pypi.yml
- macs3
- bdgbroadcall_cmd.rst
- bdgcmp_cmd.rst
- bdgdiff_cmd.rst
- bdgopt_cmd.rst
- bdgpeakcall_cmd.rst
- callpeak_cmd.rst
- callvar_cmd.rst
- cmbreps_cmd.rst
- filterdup_cmd.rst
- hmmratac_cmd.rst
- index.rst
- pileup_cmd.rst
- predictd_cmd.rst
- randsample_cmd.rst
- refinepeak_cmd.rst
- BAM.rst
- BedGraphIO.rst
- index.rst
- OutputWriter.rst
- Parser.rst
- PeakIO.rst
- BedGraph.rst
- CallPeakUnit.rst
- FixWidthTrack.rst
- HMMR_EM.rst
- HMMR_HMM.rst
- HMMR_Signal_Processing.rst
- index.rst
- PairedEndTrack.rst
- PeakDetect.rst
- PeakModel.rst
- PeakVariants.rst
- Pileup.rst
- PileupV2.rst
- PosReadsInfo.rst
- Prob.rst
- RACollection.rst
- ReadAlignment.rst
- Region.rst
- ScoreTrack.rst
- SignalProcessing.rst
- UnitigRACollection.rst
- VariantStat.rst
- Constants.rst
- index.rst
- Logger.rst
- OptValidator.rst
- index.rst
- Advanced_Step-by-step_Peak_Calling.md
- bdgbroadcall.md
- bdgcmp.md
- bdgdiff.md
- bdgopt.md
- bdgpeakcall.md
- BED.md
- bedGraph.md
- BEDPE.md
- broadPeak.md
- callpeak.md
- callpeakxls.md
- callvar.md
- callvar_algorithm.jpeg
- cmbreps.md
- cutoffanalysis.md
- fileformats_index.md
- filterdup.md
- FRAG.md
- gappedPeak.md
- hmmratac.md
- hmmratacModel.md
- INSTALL.md
- narrowPeak.md
- pileup.md
- pileup.png
- predictd.md
- qa.md
- randsample.md
- refinepeak.md
- SAMBAMBAMPE.md
- subcommands_index.md
- tutorial.md
- vcf.md
- version_benchmark.md
- CODE_OF_CONDUCT.md
- conf.py
- CONTRIBUTING.md
- index.md
- make.bat
- Makefile
- __init__.py
- bdgbroadcall_cmd.py
- bdgcmp_cmd.py
- bdgdiff_cmd.py
- bdgopt_cmd.py
- bdgpeakcall_cmd.py
- callpeak_cmd.py
- callvar_cmd.py
- cmbreps_cmd.py
- filterdup_cmd.py
- hmmratac_cmd.py
- pileup_cmd.py
- pileup_v2_cmd.py
- predictd_cmd.py
- randsample_cmd.py
- refinepeak_cmd.py
- bfc.c
- bseq.c
- bubble.c
- example.c
- fml.h
- htab.c
- htab.h
- internal.h
- khash.h
- kmer.h
- kseq.h
- ksort.h
- kstring.h
- ksw.c
- ksw.h
- kthread.c
- kvec.h
- lib
- LICENSE.txt
- mag.c
- mag.h
- Makefile
- misc.c
- mrope.c
- mrope.h
- README.md
- rld0.c
- rld0.h
- rle.c
- rle.h
- rope.c
- rope.h
- unitig.c
- __init__.py
- BAM.py
- BedGraphIO.py
- OutputWriter.py
- Parser.py
- PeakIO.py
- __init__.py
- BedGraph.py
- CallPeakUnit.py
- cPosValCalculation.c
- cPosValCalculation.h
- cPosValCalculation.pxd
- FixWidthTrack.py
- HMMR_EM.py
- HMMR_HMM.py
- HMMR_Signal_Processing.py
- PairedEndTrack.py
- PeakDetect.py
- PeakModel.py
- PeakVariants.py
- Pileup.py
- PileupV2.py
- PosReadsInfo.py
- Prob.py
- RACollection.pxd
- RACollection.py
- ReadAlignment.py
- Region.py
- ScoreTrack.py
- SignalProcessing.py
- swalign.c
- swalign.h
- UnitigRACollection.py
- VariantStat.py
- __init__.py
- Constants.py
- Logger.py
- OptValidator.py
- __init__.py
- README.md
- macs3-scATAC-pbmc-10k.ipynb
- anndata_implemetation_dev.ipynb
- macs3-scATAC-pbmc-500-anndata.ipynb
- macs3-scATAC-pbmc-500.ipynb
- benchmark_pileup_mlx.py
- benchmark_scoretrack_torch.py
- build_docs.py
- run_macs_version_survey.sh
- summarize_macs_version_survey.py
- run_callpeak_50kcontigs_peaks.narrowPeak
- run_callpeak_50kcontigs_summits.bed
- run_filterdup_result.bed
- run_pileup_ChIP.bed.bdg
- run_bdgbroadcall_w_prefix_c2.0_C1.50_l200_g30_G800_broad.bed12
- run_bdgcmp_FE.bdg
- run_bdgcmp_ppois.bdg
- common.bed
- cond1.bed
- cond2.bed
- run_bdgdiff_prefix_c3.0_common.bed
- run_bdgdiff_prefix_c3.0_cond1.bed
- run_bdgdiff_prefix_c3.0_cond2.bed
- run_bdgopt_max.bdg
- run_bdgopt_min.bdg
- run_bdgpeakcall_w_prefix_c2.0_l200_g30_peaks.narrowPeak
- run_callpeak_broad_control_lambda.bdg
- run_callpeak_broad_peaks.broadPeak
- run_callpeak_broad_peaks.gappedPeak
- run_callpeak_broad_treat_pileup.bdg
- run_callpeak_frag_barcode_peaks.narrowPeak
- run_callpeak_frag_peaks.narrowPeak
- run_callpeak_narrow0_control_lambda.bdg
- run_callpeak_narrow0_peaks.narrowPeak
- run_callpeak_narrow0_summits.bed
- run_callpeak_narrow0_treat_pileup.bdg
- run_callpeak_narrow1_control_lambda.bdg
- run_callpeak_narrow1_peaks.narrowPeak
- run_callpeak_narrow1_summits.bed
- run_callpeak_narrow1_treat_pileup.bdg
- run_callpeak_narrow2_control_lambda.bdg
- run_callpeak_narrow2_peaks.narrowPeak
- run_callpeak_narrow2_summits.bed
- run_callpeak_narrow2_treat_pileup.bdg
- run_callpeak_narrow3_control_lambda.bdg
- run_callpeak_narrow3_peaks.narrowPeak
- run_callpeak_narrow3_summits.bed
- run_callpeak_narrow3_treat_pileup.bdg
- run_callpeak_narrow4_control_lambda.bdg
- run_callpeak_narrow4_peaks.narrowPeak
- run_callpeak_narrow4_summits.bed
- run_callpeak_narrow4_treat_pileup.bdg
- run_callpeak_narrow5_control_lambda.bdg
- run_callpeak_narrow5_peaks.narrowPeak
- run_callpeak_narrow5_summits.bed
- run_callpeak_narrow5_treat_pileup.bdg
- run_callpeak_narrow_revert_control_lambda.bdg
- run_callpeak_narrow_revert_peaks.narrowPeak
- run_callpeak_narrow_revert_summits.bed
- run_callpeak_narrow_revert_treat_pileup.bdg
- run_callpeak_bampe_broad_control_lambda.bdg
- run_callpeak_bampe_broad_peaks.broadPeak
- run_callpeak_bampe_broad_peaks.gappedPeak
- run_callpeak_bampe_broad_treat_pileup.bdg
- run_callpeak_bedpe_broad_control_lambda.bdg
- run_callpeak_bedpe_broad_peaks.broadPeak
- run_callpeak_bedpe_broad_peaks.gappedPeak
- run_callpeak_bedpe_broad_treat_pileup.bdg
- run_callpeak_bampe_narrow_control_lambda.bdg
- run_callpeak_bampe_narrow_peaks.narrowPeak
- run_callpeak_bampe_narrow_summits.bed
- run_callpeak_bampe_narrow_treat_pileup.bdg
- run_callpeak_bedpe_narrow_control_lambda.bdg
- run_callpeak_bedpe_narrow_peaks.narrowPeak
- run_callpeak_bedpe_narrow_summits.bed
- run_callpeak_bedpe_narrow_treat_pileup.bdg
- run_callpeak_pe_narrow_onlychip_control_lambda.bdg
- run_callpeak_pe_narrow_onlychip_peaks.narrowPeak
- run_callpeak_pe_narrow_onlychip_summits.bed
- run_callpeak_pe_narrow_onlychip_treat_pileup.bdg
- PEsample.vcf
- run_cmbreps_fisher.bdg
- run_cmbreps_max.bdg
- run_cmbreps_mean.bdg
- run_filterdup_result.bed
- run_filterdup_result_pe.bedpe
- hmmratac_scatac_test_accessible_regions.narrowPeak
- hmmratac_yeast500k_accessible_regions.narrowPeak
- hmmratac_yeast500k_bedpe_accessible_regions.narrowPeak
- hmmratac_yeast500k_bedpe_poisson_accessible_regions.narrowPeak
- hmmratac_yeast500k_load_hmm_model_accessible_regions.narrowPeak
- hmmratac_yeast500k_load_training_regions_accessible_regions.narrowPeak
- hmmratac_yeast500k_poisson_accessible_regions.narrowPeak
- hmmratac_yeast500k_poisson_load_hmm_model_accessible_regions.narrowPeak
- hmmratac_yeast500k_poisson_load_training_regions_accessible_regions.narrowPeak
- run_pileup_ChIP.bed.bdg
- run_pileup_ChIPPE.bampe.bdg
- run_pileup_ChIPPE.bedpe.bdg
- run_pileup_CTRL.bed.bdg
- run_pileup_CTRLPE.bampe.bdg
- run_pileup_CTRLPE.bedpe.bdg
- run_predictd.txt
- run_predictd_bampe.txt
- run_predictd_bedpe.txt
- run_refinepeak_w_ofile.bed
- run_refinepeak_w_prefix_refinepeak.bed
- barcodes.txt
- callvar_testing.narrowPeak
- cmdlinetest
- cmdlinetest-nohmmratac
- contigs50k.bed.gz
- CTCF_12878_5M.bed.gz
- CTCF_PE_ChIP_chr22_50k.bam
- CTCF_PE_ChIP_chr22_50k.bam.bai
- CTCF_PE_ChIP_chr22_50k.bedpe.gz
- CTCF_PE_CTRL_chr22_50k.bam
- CTCF_PE_CTRL_chr22_50k.bam.bai
- CTCF_PE_CTRL_chr22_50k.bedpe.gz
- CTCF_SE_ChIP_chr22_50k.bed.gz
- CTCF_SE_CTRL_chr22_50k.bed.gz
- hg19.len
- Input_12878_5M.bed.gz
- jaccard.py
- large_training_data.txt
- large_training_lengths.txt
- prockreport
- pyprofile
- pyprofile_stat
- small_prediction_data.txt
- small_prediction_lengths.txt
- small_prediction_results.txt
- small_prediction_results_poisson.txt
- test.fragments.tsv.gz
- test_BAMBAI.py
- test_BedGraph.py
- test_BedGraphIO.py
- test_CallPeakUnit.py
- test_FixWidthTrack.py
- test_HMMR_HMM.py
- test_HMMR_poisson.py
- test_online.py
- test_PairedEndTrack.py
- test_Parser.py
- test_PeakDetect.py
- test_PeakIO.py
- test_PeakModel.py
- test_Pileup.py
- test_Prob.py
- test_Region.py
- test_ScoreTrack.py
- test_SignalProcessing.py
- tiny.bam
- tiny.bam.bai
- tiny.bed.gz
- tiny.bedpe.gz
- tiny.frag.tsv.gz
- tiny.sam.gz
- yeast_500k_SRR1822137.bam
- yeast_500k_SRR1822137.barcode.txt
- yeast_500k_SRR1822137.bedpe.gz
- yeast_500k_SRR1822137.frag.gz
- .dockerignore
- .gitignore
- .gitmodules
- ChangeLog
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- LICENSE
- MANIFEST.in
- pyproject.toml
- README.md
- requirements.txt
- setup.py
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/macs3-project/MACS
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd MACS
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. Python
쉬움 추천사전 준비물
pip install -r requirements.txt
requirements.txt 등에 명시된 파이썬 라이브러리를 설치합니다.
jupyter notebook
브라우저에서 노트북(.ipynb) 파일들을 열람하고 실행할 수 있는 Jupyter 화면을 켭니다.
에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.
3. Make
보통사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Make Linux/macOS는 보통 기본 설치되어 있습니다. Windows는 별도 설치(예: MSYS2, WSL)가 필요합니다.
⚠️ 이 프로젝트는 규모가 큰 저장소라, 이 방법이 실제 핵심 제품이 아니라 내부 하위 패키지를 가리키는 것일 수 있습니다. README 전체를 함께 확인해보세요.
cd MACS3/fermi-lite
이 프로젝트의 관련 파일이 하위 폴더 안에 있어서, 먼저 그 폴더로 이동합니다.
make
생성된 빌드 설정을 바탕으로 실제 컴파일을 진행해 실행 파일을 만듭니다.
에러 없이 끝나면 성공입니다. 생성된 실행 파일을 직접 실행해보세요.
// repository documentation
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