Tsrchitect
WebSearch: Home; Install; Help; Developers; About WebDec 16, 2024 · TSRchitect is an open-source bioinformatics package that is intended to support large-scale, reproducible analysis of TSS profiling data in a broad array of …
Tsrchitect
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WebNov 10, 2024 · TSRchitect, the package we’ll use for this analysis, is an R package available in the Bioconductor suite of genomics tools . It makes use of existing packages and data … WebTSRchitect User’s Guide TSRchitect User’s Guide R. Taylor Raborn and Volker P. Brendel Department of Biology, Indiana University First edition 25 January 2024 Updated 27 June …
WebPackages removed with Bioconductor 3.3 release. No packages were removed with this release. 17 packages were marked as deprecated, to be removed in the next release. WebNov 4, 2024 · TSRchitect and CAGEr also include functions (inputToTSS(), getCTSSs(), respectively) for obtaining CTSSs from BAM-files from within R, with CAGEr having the option of correcting for G-bias when mapping. CAGEfightR can analyze many types of 5’-end data, as long as they can be represented in a format similar to CTSSs.
WebMar 28, 2015 · TSRchitect Public Promoter identification from diverse types of large-scale TSS profiling data R 1 GPL-3.0 4 2 1 Updated Jan 3, 2024. GoSTRIPES Public Computational workflows for STRIPE-seq data analyses Perl 4 5 0 0 Updated Dec 25, 2024. bgSingularityHub Public WebTSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq). In addition, (new with version 1.3.0) TSRchitect provides the ability to import aligned EST and ...
WebTSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end …
WebNov 8, 2024 · TSRchitect / getTitle-methods: *getTitle* getTitle-methods: *getTitle* In TSRchitect: Promoter identification from large-scale TSS profiling data. Description … binghamton club soccerczech cyber security working groupWebCurrently, these are BED files, delimited tables, and TSRchitect tssObjects. To import TSRs from files, a sample sheet must first be created. The sample sheet can be a data.frame or tabular file. It should have three columns: sample_name, file_1, ... binghamton college baseballWebThe final BAMs are also ready for TSS and TSS cluster (TSR or cTSS) analysis. There are many great software suites available for this, including TSRchitect, CAGEr, ADAPT-CAGE, and CAGEfightR. For convenience, gostripes includes some rudimentary functions for basic TSS and TSR calling. binghamton code enforcement officeWebFeb 3, 2024 · Finally, TSRchitect imports annotation files, allowing the user to associate identified promoters with genes and other genomic features. Three detailed examples of … binghamton classic carsWebTSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end … czech customs and traditionsWebDec 30, 2024 · TSRchitect 1.20.0:: DESCRIPTION. TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS … binghamton club menu