CRED: a rapid peak caller for Chem-seq data
نویسندگان
چکیده
منابع مشابه
A Comparison of Peak Callers Used for DNase-Seq Data
Genome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements. A variety of algorithms have been developed to identify regions of open chromatin from raw sequence-tag data, which has motivated us to assess and compare their performance. In this study, four published, publi...
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Motivation and Objectives ChIP-Seq has rapidly become the dominant experimental technique in functional genomic and epigenomic research. Statistical analysis of ChIP-Seq data sets however remains challenging, due to the highly structured nature of the data and the paucity of replicates. Current approaches to detect differentially bound or modified genomic regions are mainly borrowed from RNA-Se...
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هدف اصلی از این تحقیق به دست آوردن و مقایسه حق بیمه باورمندی در مدل های شمارشی گزارش نشده برای داده های طولی می باشد. در این تحقیق حق بیمه های پبش گویی بر اساس توابع ضرر مربع خطا و نمایی محاسبه شده و با هم مقایسه می شود. تمایل به گرفتن پاداش و جایزه یکی از دلایل مهم برای گزارش ندادن تصادفات می باشد و افراد برای استفاده از تخفیف اغلب از گزارش تصادفات با هزینه پائین خودداری می کنند، در این تحقیق ...
15 صفحه اولFeatures of ChIP-seq data peak calling algorithms with good operating characteristics Running Title: Benchmark ChIP-seq peak calling algorithms
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in analysis of these data. Peak-calling consists of two sub-problems: identifying candidate peaks and testing candidate . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/f...
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3 Example: Obtaining differentially bound sites 3 3.1 Reading in the peaksets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3.2 Counting reads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.3 Establishing a contrast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...
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ژورنال
عنوان ژورنال: Journal of Open Source Software
سال: 2019
ISSN: 2475-9066
DOI: 10.21105/joss.01423