├── .dir-locals.el ├── .gitignore ├── COPYRIGHT ├── LICENSE ├── MAINTENANCE.rst ├── Makefile ├── README.rst ├── data └── tss │ ├── README.md │ ├── get_human_mouse_rat_orthologues.R │ ├── hg19.tss.refseq.bed.gz │ ├── hg19.tss.refseq.housekeeping.all.bed.gz │ ├── hg19.tss.refseq.housekeeping.ortho.bed.gz │ ├── make_tss.R │ ├── mm9.tss.refseq.bed.gz │ ├── mm9.tss.refseq.housekeeping.ortho.bed.gz │ ├── rn5.tss.refseq.bed.gz │ └── rn5.tss.refseq.housekeeping.ortho.bed.gz ├── debian ├── changelog ├── compat ├── control ├── copyright ├── docs ├── rules └── source │ └── format ├── docs ├── css │ ├── ataqv.css │ └── normalize.css ├── demo │ ├── css │ │ ├── ataqv.css │ │ ├── datatables.buttons.min.css │ │ ├── datatables.fontawesome.css │ │ ├── datatables.min.css │ │ ├── font-awesome.min.css │ │ └── normalize.css │ ├── data │ │ ├── SRS438193_SRR891268_1.json.gz │ │ ├── SRS438194_SRR891269_1.json.gz │ │ ├── SRS438195_SRR891270_1.json.gz │ │ ├── SRS438196_SRR891271_1.json.gz │ │ ├── SRS438197_SRR891272_1.json.gz │ │ ├── SRS438198_SRR891273_1.json.gz │ │ ├── SRS438199_SRR891274_1.json.gz │ │ ├── SRS438200_SRR891275_1.json.gz │ │ ├── SRS438201_SRR891276_1.json.gz │ │ ├── SRS438202_SRR891277_1.json.gz │ │ ├── SRS438203_SRR891278_1.json.gz │ │ ├── SRS438204_SRR891279_1.json.gz │ │ └── SRS438205_SRR891280_1.json.gz │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── sourcesanspro-regular.woff │ │ ├── sourcesanspro-regularit.woff │ │ ├── sourcesanspro-semibold.woff │ │ └── sourcesanspro-semiboldit.woff │ ├── index.html │ └── js │ │ ├── ataqv.js │ │ ├── configuration.js │ │ ├── d3.min.js │ │ ├── datatables.min.js │ │ └── jszip.min.js └── index.html ├── src ├── cpp │ ├── Exceptions.hpp │ ├── Features.cpp │ ├── Features.hpp │ ├── HTS.cpp │ ├── HTS.hpp │ ├── IO.cpp │ ├── IO.hpp │ ├── Metrics.cpp │ ├── Metrics.hpp │ ├── Peaks.cpp │ ├── Peaks.hpp │ ├── Utils.cpp │ ├── Utils.hpp │ ├── Version.hpp │ ├── ataqv.cpp │ ├── catch.hpp │ ├── json.hpp │ ├── run_ataqv_tests.cpp │ ├── test_features.cpp │ ├── test_hts.cpp │ ├── test_io.cpp │ ├── test_metrics.cpp │ ├── test_peaks.cpp │ └── test_utils.cpp ├── scripts │ ├── make_ataqv_pipeline │ ├── mkarv │ ├── run_ataqv_example │ └── srvarv └── web │ ├── css │ ├── ataqv.css │ ├── datatables.buttons.min.css │ ├── datatables.fontawesome.css │ ├── datatables.min.css │ ├── font-awesome.min.css │ └── normalize.css │ ├── fonts │ ├── FontAwesome.otf │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ ├── fontawesome-webfont.woff │ ├── fontawesome-webfont.woff2 │ ├── sourcesanspro-regular.woff │ ├── sourcesanspro-regularit.woff │ ├── sourcesanspro-semibold.woff │ └── sourcesanspro-semiboldit.woff │ ├── index.html │ └── js │ ├── ataqv.js │ ├── d3.min.js │ ├── datatables.min.js │ └── jszip.min.js └── testdata ├── SRR891275.bam ├── SRR891275.bam.bai ├── SRR891275.peaks.gz ├── SRR891278.bam ├── SRR891278.peaks.gz ├── exclude.dac.bed.gz ├── exclude.duke.bed.gz ├── hg19.tss.refseq.bed.gz ├── mktd.sh ├── test.bam ├── test.bam.bai └── test.peaks.gz /.dir-locals.el: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/.dir-locals.el -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/.gitignore -------------------------------------------------------------------------------- /COPYRIGHT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/COPYRIGHT -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/LICENSE -------------------------------------------------------------------------------- /MAINTENANCE.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/MAINTENANCE.rst -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/Makefile -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/README.rst -------------------------------------------------------------------------------- /data/tss/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/README.md -------------------------------------------------------------------------------- /data/tss/get_human_mouse_rat_orthologues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/get_human_mouse_rat_orthologues.R -------------------------------------------------------------------------------- /data/tss/hg19.tss.refseq.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/hg19.tss.refseq.bed.gz -------------------------------------------------------------------------------- /data/tss/hg19.tss.refseq.housekeeping.all.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/hg19.tss.refseq.housekeeping.all.bed.gz -------------------------------------------------------------------------------- /data/tss/hg19.tss.refseq.housekeeping.ortho.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/hg19.tss.refseq.housekeeping.ortho.bed.gz -------------------------------------------------------------------------------- /data/tss/make_tss.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/make_tss.R -------------------------------------------------------------------------------- /data/tss/mm9.tss.refseq.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/mm9.tss.refseq.bed.gz -------------------------------------------------------------------------------- /data/tss/mm9.tss.refseq.housekeeping.ortho.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/mm9.tss.refseq.housekeeping.ortho.bed.gz -------------------------------------------------------------------------------- /data/tss/rn5.tss.refseq.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/rn5.tss.refseq.bed.gz -------------------------------------------------------------------------------- /data/tss/rn5.tss.refseq.housekeeping.ortho.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/data/tss/rn5.tss.refseq.housekeeping.ortho.bed.gz -------------------------------------------------------------------------------- /debian/changelog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/debian/changelog -------------------------------------------------------------------------------- /debian/compat: -------------------------------------------------------------------------------- 1 | 9 2 | -------------------------------------------------------------------------------- /debian/control: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/debian/control -------------------------------------------------------------------------------- /debian/copyright: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/debian/copyright -------------------------------------------------------------------------------- /debian/docs: -------------------------------------------------------------------------------- 1 | README.rst -------------------------------------------------------------------------------- /debian/rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/debian/rules -------------------------------------------------------------------------------- /debian/source/format: -------------------------------------------------------------------------------- 1 | 3.0 (quilt) 2 | -------------------------------------------------------------------------------- /docs/css/ataqv.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/css/ataqv.css -------------------------------------------------------------------------------- /docs/css/normalize.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/css/normalize.css -------------------------------------------------------------------------------- /docs/demo/css/ataqv.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/ataqv.css -------------------------------------------------------------------------------- /docs/demo/css/datatables.buttons.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/datatables.buttons.min.css -------------------------------------------------------------------------------- /docs/demo/css/datatables.fontawesome.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/datatables.fontawesome.css -------------------------------------------------------------------------------- /docs/demo/css/datatables.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/datatables.min.css -------------------------------------------------------------------------------- /docs/demo/css/font-awesome.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/font-awesome.min.css -------------------------------------------------------------------------------- /docs/demo/css/normalize.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/css/normalize.css -------------------------------------------------------------------------------- /docs/demo/data/SRS438193_SRR891268_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438193_SRR891268_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438194_SRR891269_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438194_SRR891269_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438195_SRR891270_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438195_SRR891270_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438196_SRR891271_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438196_SRR891271_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438197_SRR891272_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438197_SRR891272_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438198_SRR891273_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438198_SRR891273_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438199_SRR891274_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438199_SRR891274_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438200_SRR891275_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438200_SRR891275_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438201_SRR891276_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438201_SRR891276_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438202_SRR891277_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438202_SRR891277_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438203_SRR891278_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438203_SRR891278_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438204_SRR891279_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438204_SRR891279_1.json.gz -------------------------------------------------------------------------------- /docs/demo/data/SRS438205_SRR891280_1.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/data/SRS438205_SRR891280_1.json.gz -------------------------------------------------------------------------------- /docs/demo/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /docs/demo/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /docs/demo/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /docs/demo/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /docs/demo/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /docs/demo/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /docs/demo/fonts/sourcesanspro-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/sourcesanspro-regular.woff -------------------------------------------------------------------------------- /docs/demo/fonts/sourcesanspro-regularit.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/sourcesanspro-regularit.woff -------------------------------------------------------------------------------- /docs/demo/fonts/sourcesanspro-semibold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/sourcesanspro-semibold.woff -------------------------------------------------------------------------------- /docs/demo/fonts/sourcesanspro-semiboldit.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/fonts/sourcesanspro-semiboldit.woff -------------------------------------------------------------------------------- /docs/demo/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/index.html -------------------------------------------------------------------------------- /docs/demo/js/ataqv.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/js/ataqv.js -------------------------------------------------------------------------------- /docs/demo/js/configuration.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/js/configuration.js -------------------------------------------------------------------------------- /docs/demo/js/d3.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/js/d3.min.js -------------------------------------------------------------------------------- /docs/demo/js/datatables.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/js/datatables.min.js -------------------------------------------------------------------------------- /docs/demo/js/jszip.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/demo/js/jszip.min.js -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/docs/index.html -------------------------------------------------------------------------------- /src/cpp/Exceptions.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Exceptions.hpp -------------------------------------------------------------------------------- /src/cpp/Features.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Features.cpp -------------------------------------------------------------------------------- /src/cpp/Features.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Features.hpp -------------------------------------------------------------------------------- /src/cpp/HTS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/HTS.cpp -------------------------------------------------------------------------------- /src/cpp/HTS.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/HTS.hpp -------------------------------------------------------------------------------- /src/cpp/IO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/IO.cpp -------------------------------------------------------------------------------- /src/cpp/IO.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/IO.hpp -------------------------------------------------------------------------------- /src/cpp/Metrics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Metrics.cpp -------------------------------------------------------------------------------- /src/cpp/Metrics.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Metrics.hpp -------------------------------------------------------------------------------- /src/cpp/Peaks.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Peaks.cpp -------------------------------------------------------------------------------- /src/cpp/Peaks.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Peaks.hpp -------------------------------------------------------------------------------- /src/cpp/Utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Utils.cpp -------------------------------------------------------------------------------- /src/cpp/Utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Utils.hpp -------------------------------------------------------------------------------- /src/cpp/Version.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/Version.hpp -------------------------------------------------------------------------------- /src/cpp/ataqv.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/ataqv.cpp -------------------------------------------------------------------------------- /src/cpp/catch.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/catch.hpp -------------------------------------------------------------------------------- /src/cpp/json.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/json.hpp -------------------------------------------------------------------------------- /src/cpp/run_ataqv_tests.cpp: -------------------------------------------------------------------------------- 1 | #define CATCH_CONFIG_MAIN 2 | #include "catch.hpp" 3 | -------------------------------------------------------------------------------- /src/cpp/test_features.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_features.cpp -------------------------------------------------------------------------------- /src/cpp/test_hts.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_hts.cpp -------------------------------------------------------------------------------- /src/cpp/test_io.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_io.cpp -------------------------------------------------------------------------------- /src/cpp/test_metrics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_metrics.cpp -------------------------------------------------------------------------------- /src/cpp/test_peaks.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_peaks.cpp -------------------------------------------------------------------------------- /src/cpp/test_utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/cpp/test_utils.cpp -------------------------------------------------------------------------------- /src/scripts/make_ataqv_pipeline: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/scripts/make_ataqv_pipeline -------------------------------------------------------------------------------- /src/scripts/mkarv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/scripts/mkarv -------------------------------------------------------------------------------- /src/scripts/run_ataqv_example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/scripts/run_ataqv_example -------------------------------------------------------------------------------- /src/scripts/srvarv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/scripts/srvarv -------------------------------------------------------------------------------- /src/web/css/ataqv.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/ataqv.css -------------------------------------------------------------------------------- /src/web/css/datatables.buttons.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/datatables.buttons.min.css -------------------------------------------------------------------------------- /src/web/css/datatables.fontawesome.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/datatables.fontawesome.css -------------------------------------------------------------------------------- /src/web/css/datatables.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/datatables.min.css -------------------------------------------------------------------------------- /src/web/css/font-awesome.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/font-awesome.min.css -------------------------------------------------------------------------------- /src/web/css/normalize.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/css/normalize.css -------------------------------------------------------------------------------- /src/web/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /src/web/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /src/web/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /src/web/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /src/web/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /src/web/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /src/web/fonts/sourcesanspro-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/sourcesanspro-regular.woff -------------------------------------------------------------------------------- /src/web/fonts/sourcesanspro-regularit.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/sourcesanspro-regularit.woff -------------------------------------------------------------------------------- /src/web/fonts/sourcesanspro-semibold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/sourcesanspro-semibold.woff -------------------------------------------------------------------------------- /src/web/fonts/sourcesanspro-semiboldit.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/fonts/sourcesanspro-semiboldit.woff -------------------------------------------------------------------------------- /src/web/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/index.html -------------------------------------------------------------------------------- /src/web/js/ataqv.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/js/ataqv.js -------------------------------------------------------------------------------- /src/web/js/d3.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/js/d3.min.js -------------------------------------------------------------------------------- /src/web/js/datatables.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/js/datatables.min.js -------------------------------------------------------------------------------- /src/web/js/jszip.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/src/web/js/jszip.min.js -------------------------------------------------------------------------------- /testdata/SRR891275.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/SRR891275.bam -------------------------------------------------------------------------------- /testdata/SRR891275.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/SRR891275.bam.bai -------------------------------------------------------------------------------- /testdata/SRR891275.peaks.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/SRR891275.peaks.gz -------------------------------------------------------------------------------- /testdata/SRR891278.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/SRR891278.bam -------------------------------------------------------------------------------- /testdata/SRR891278.peaks.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/SRR891278.peaks.gz -------------------------------------------------------------------------------- /testdata/exclude.dac.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/exclude.dac.bed.gz -------------------------------------------------------------------------------- /testdata/exclude.duke.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/exclude.duke.bed.gz -------------------------------------------------------------------------------- /testdata/hg19.tss.refseq.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/hg19.tss.refseq.bed.gz -------------------------------------------------------------------------------- /testdata/mktd.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/mktd.sh -------------------------------------------------------------------------------- /testdata/test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/test.bam -------------------------------------------------------------------------------- /testdata/test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/test.bam.bai -------------------------------------------------------------------------------- /testdata/test.peaks.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParkerLab/ataqv/HEAD/testdata/test.peaks.gz --------------------------------------------------------------------------------