doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a s
インストールする前に、エージェントに与えられる指示の中身を確認できます。
library(doubletrouble)
library(syntenet)
# Load example data
data(yeast_seq)
data(yeast_annot)
data(diamond_intra)
# Prepare input data
pdata <- process_input(yeast_seq, yeast_annot)
# Classify gene pairs using the standard scheme
c_standard <- classify_gene_pairs(
annotation = pdata$annotation,
blast_list = diamond_intra,
scheme = "standard"
)
# Calculate duplicate frequencies
table(c_standard$Scerevisiae$type)
Note: Inputs are processed protein sequences and gene annotations along with intraspecies DIAMOND search results; output is a list of classified duplicated gene pairs.
classify_gene_pairs.syntenet functions like process_input and run_diamond instead.AAStringSet objects containing translated sequences of the primary transcripts.GRanges objects containing genomic coordinates of all features.run_diamond).GRangesList object).setequal(names(seqs), names(annotation)).collapse_bidirectional_hits before classification.syntenet for synteny detection and running DIAMOND alignments.まだレビューはありません。使ってみた感想をお寄せください。
概要と使いどころ
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
日本語の概要は準備中です。原文の説明を表示しています。
This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
日本語の概要は準備中です。原文の説明を表示しています。
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
日本語の概要は準備中です。原文の説明を表示しています。
apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
日本語の概要は準備中です。原文の説明を表示しています。
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
日本語の概要は準備中です。原文の説明を表示しています。
AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
日本語の概要は準備中です。原文の説明を表示しています。