文件名称：FFPEsig:FFPEsig手稿的代码和数据
文件大小：7.08MB
文件格式：ZIP
更新时间：2024-04-03 01:06:39
JupyterNotebook
聚四氟乙烯
FFPEsig使用FFPE签名作为噪声配置文件来校正从给定FFPE WGS样本中观察到的突变计数。
要运行FFPEsig，请执行以下操作：
下载
安装和所需的软件包，包括pandas，numpy，matplotlib，seaborn。
运行命令行：
python FFPEsig.py [--input|-i]
【文件预览】：
FFPEsig-main
----FFPEsig.py(17KB)
----setup.py(15KB)
----README.md(2KB)
----Data()
--------study1_gene_seq.fa(65KB)
--------WGS_PCAWG.96.csv(859KB)
--------SBS_signatures.csv(56KB)
--------study1_BlockageGroup_mutCounts.csv(5KB)
--------study2_gene_seq.fa(2.42MB)
--------CRC_MSI.samples(243B)
--------repaired_profiles_corrected.csv(842KB)
--------fixiationgroup.txt(6.19MB)
--------Refitting_Activities_Results_80c_96c.csv(711KB)
--------Different_FFPEloads()
--------FFPE_signatures_stats.csv(7KB)
--------WGS_FFPEsamples.SBS96.csv(3KB)
--------Refitting_Accuracy_80c_96c.csv(91KB)
--------study1_BaselineGroup_mutCounts.csv(15KB)
--------CRC_POLE.samples(217B)
--------WGS_PCAWG.activities.csv(454KB)
--------WGS_opp.csv(2KB)
--------unrepaired_profiles_corrected.csv(842KB)
--------LocalFFPE_BeforeCorrection_profiles.csv(2KB)
--------study2_FFPEonly_mutCounts.csv(3KB)
--------simulated_PCAWG_FFPE_repaired.csv(945KB)
--------simulated_PCAWG_FFPE_unrepaired.csv(906KB)
--------study1_FixationGroup_mutCounts.csv(6KB)
----Copyright.txt(34KB)
----docs()
--------Comparing_refitting_results_of_96c_80c_sig.html(953KB)
--------index.html(45B)
--------Correcting_FFPEnoise_in_WGS_FFPE_CRCs.html(1.17MB)
--------Correctting_FFPEnoise_in_SimulatedFFPEs_from_PCAWG.html(718KB)
--------FFPEsig_discovery.html(924KB)
----Notebooks()
--------Comparing_refitting_results_of_96c_80c_sig.ipynb(587KB)
--------FFPEsig_discovery.ipynb(503KB)
--------Correctting_FFPEnoise_in_SimulatedFFPEs_from_PCAWG.ipynb(385KB)
--------Correcting_FFPEnoise_in_WGS_FFPE_CRCs.ipynb(759KB)
----FFPEsig_OUTPUT()
--------ColoRect-AdenoCA::SP21528_before_correction.pdf(21KB)
--------ColoRect-AdenoCA::SP21528_corrected_profile.csv(342B)
--------ColoRect-AdenoCA::SP21528_all_solutions.csv(176KB)
--------ColoRect-AdenoCA::SP21528_after_correction.pdf(20KB)