This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/hermes

Package: hermes 1.7.2

Daniel Sabanés Bové

hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.

Authors:Daniel Sabanés Bové [aut, cre], Namrata Bhatia [aut], Stefanie Bienert [aut], Benoit Falquet [aut], Haocheng Li [aut], Jeff Luong [aut], Lyndsee Midori Zhang [aut], Alex Richardson [aut], Simona Rossomanno [aut], Tim Treis [aut], Mark Yan [aut], Naomi Chang [aut], Chendi Liao [aut], Carolyn Zhang [aut], Joseph N. Paulson [aut], F. Hoffmann-La Roche AG [cph, fnd]

hermes_1.7.2.tar.gz
hermes_1.7.2.zip(r-4.7)hermes_1.7.2.zip(r-4.6)hermes_1.7.2.zip(r-4.5)
hermes_1.7.2.tgz(r-4.6-any)hermes_1.7.2.tgz(r-4.5-any)
hermes_1.7.2.tar.gz(r-4.7-any)hermes_1.7.2.tar.gz(r-4.6-any)
hermes_1.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hermes/json (API)

# Install 'hermes' in R:

install.packages('hermes', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/insightsengineering/hermes/issues

Pkgdown/docs site:https://insightsengineering.github.io

Datasets:

expression_set - Example 'ExpressionSet' Data
hermes_data - Example 'HermesData' Data
multi_assay_experiment - Example 'MultiAssayExperiment' Data
summarized_experiment - Example 'SummarizedExperiment' Data

On BioConductor:hermes-1.17.0(bioc 3.24)hermes-1.16.0(bioc 3.23)

rnaseq differentialexpression normalization preprocessing qualitycontrol rna-seq statistical-engineering

7.32 score 12 stars 1 packages 45 scripts 92 exports 117 dependencies

Last updated from:fdf4ec82e3 (on v1.7.2). Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	ERROR	427
source / vignettes	OK	355
linux-release-x86_64	ERROR	439
macos-release-arm64	ERROR	337
macos-oldrel-arm64	ERROR	401
windows-devel	ERROR	474
windows-release	ERROR	619
windows-oldrel	ERROR	444
wasm-release	OK	180

Exports:.ConnectionBiomart .row_data_annotation_cols %>%add_quality_flags annotation annotation<-assert_proportion autoplot calc_pca cat_with_newline check_proportion col_data_with_genes colMeanZscores colPrinComp1 connect_biomart control_normalize control_quality correlate counts counts<-cut_quantile df_cols_to_factor diff_expression draw_barplot draw_boxplot draw_genes_barplot draw_heatmap draw_libsize_densities draw_libsize_hist draw_libsize_qq draw_nonzero_boxplot draw_scatterplot expect_proportion extraColDataNames extraRowDataNames filter gene_spec genes GeneSpec get_low_depth get_low_expression get_tech_failure h_all_duplicated h_cpm h_df_factors_with_explicit_na h_diff_expr_deseq2 h_diff_expr_voom h_draw_boxplot_df h_ensembl_to_entrez_ids h_get_annotation_biomart h_get_granges_by_id h_get_size_biomart h_has_req_annotations h_low_depth_flag h_low_expression_flag h_map_pos h_parens h_pca_df_r2_matrix h_pca_var_rsquared h_rlog h_rpkm h_short_list h_strip_prefix h_tech_failure_flag h_tpm h_unique_labels h_voom h_vst HermesData HermesDataFromMatrix inner_join_cdisc is_class is_constant is_counts_vector is_hermes_data is_list_with isEmpty lapply metadata metadata<-normalize one_provided prefix query rename samples set_tech_failure show summary test_proportion top_genes wrap_in_mae

Dependencies:abind AnnotationDbi askpass assertthat backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 blob cachem checkmate circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 digest doParallel dplyr edgeR EnvStats farver fastmap filelock forcats foreach formatR futile.logger futile.options generics GenomicRanges GetoptLong ggfortify ggplot2 ggrepel GlobalOptions glue gridExtra gtable hms httr httr2 IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment nortest openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo Rdpack rjson rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr xml2 XVector

Introduction to hermes

Rendered fromhermes.Rmdusingknitr::rmarkdown

Last update: 2024-06-27
Started: 2022-04-07

Help page	Topics
'hermes' Package	hermes-package hermes
Add Quality Flags	add_quality_flags get_low_depth get_low_expression get_tech_failure h_low_depth_flag h_low_expression_flag h_tech_failure_flag
Checks Whether All Missing	all_na
Annotation Accessor and Setter	.row_data_annotation_cols annotation annotation,AnyHermesData-method annotation<-,AnyHermesData,DataFrame-method
Standard Assertion Arguments	assertion_arguments
Additional Assertions for 'assert_that'	assertions is_class is_constant is_counts_vector is_hermes_data is_list_with one_provided
All Standard Plots in Default Setting	autoplot,AnyHermesData-method plot_all
Principal Components Analysis Calculation	.HermesDataPca calc_pca HermesDataPca HermesDataPca-class
Concatenate and Print with Newline	cat_with_newline
Column Binding of 'AnyHermesData' Objects	cbind
Check for proportion	assert_proportion check_proportion expect_proportion test_proportion
Sample Variables with Selected Gene Information	col_data_with_genes
Mean Z-score Gene Signature	colMeanZscores
First Principal Component (PC1) Gene Signature	colPrinComp1
Connection to 'BioMart'	.ConnectionBiomart ConnectionBiomart ConnectionBiomart-class connect_biomart
Control Settings for Counts Normalization	control_normalize
Control for Specified Quality Flags	control_quality
Generic Function for Correlation Calculations	correlate
Correlation between Sample Counts of 'AnyHermesData'	.HermesDataCor autoplot,HermesDataCor-method calc_cor correlate,AnyHermesData-method HermesDataCor HermesDataCor-class
Correlation of Principal Components with Sample Variables	.HermesDataPcaCor autoplot,HermesDataPcaCor-method correlate,HermesDataPca-method HermesDataPcaCor HermesDataPcaCor-class pca_cor_samplevar
Counts Accessor and Setter	counts counts,AnyHermesData-method counts<-,AnyHermesData,matrix-method
Cutting a Numeric Vector into a Factor of Quantile Bins	cut_quantile
Conversion of Eligible Columns to Factor Variables in a 'DataFrame'	df_cols_to_factor
Differential Expression Analysis	.HermesDataDiffExpr autoplot,HermesDataDiffExpr-method diff_expression HermesDataDiffExpr HermesDataDiffExpr-class
Barplot for Gene Expression Percentiles	draw_barplot
Boxplot for Gene Expression Values	draw_boxplot h_draw_boxplot_df
Stacked Barplot of Low Expression Genes by Chromosome	draw_genes_barplot
Heatmap for Gene Expression Counts	draw_heatmap
Density Plot of (Log) Counts Distributions	draw_libsize_densities
Histogram of Library Sizes	draw_libsize_hist
Q-Q Plot of Library Sizes	draw_libsize_qq
Boxplot of Non-Zero Genes	draw_nonzero_boxplot
Scatterplot for Gene Expression Values	draw_scatterplot
Example 'ExpressionSet' Data	expression_set
Extra Variable Names Accessor Methods	extraColDataNames extraColDataNames,AnyHermesData-method extraRowDataNames extraRowDataNames,AnyHermesData-method extra_data_names
Filter 'AnyHermesData' on Subset Passing Default QC Flags	filter filter,AnyHermesData-method filter,data.frame-method filter,ts-method
'GeneSpec' Constructor	gene_spec
Gene IDs Accessor	genes genes,AnyHermesData-method
R6 Class Representing a Gene (Signature) Specification	GeneSpec
Finding All Duplicates in Vector	h_all_duplicated
Conversion to Factors with Explicit Missing Level in a 'data.frame'	h_df_factors_with_explicit_na
'DESeq2' Differential Expression Analysis	h_diff_expr_deseq2
'limma'/voom Differential Expression Analysis	h_diff_expr_voom
Translation of 'Ensembl' to 'Entrez' Gene IDs	h_ensembl_to_entrez_ids
Get Annotations from 'BioMart'	h_get_annotation_biomart
Conversion of 'BioMart' Coordinates into 'GRanges'	h_get_granges_by_id
Total Length of All Exons for Genes	h_get_size_biomart
Predicate for Required Annotations	h_has_req_annotations
Helper Function For Matching Map Values to Names	h_map_pos
Parenthesize a Character Vector	h_parens
Calculation of R2 Matrix between Sample Variables and Principal Components	h_pca_df_r2_matrix
Calculation of R2 between Sample Variable and Principal Components	h_pca_var_rsquared
Make a Short List of a Character Vector	h_short_list
Stripping Prefix from Gene IDs	h_strip_prefix
Creation of Unique Labels	h_unique_labels
Example 'HermesData' Data	hermes_data
'HermesData' and 'RangedHermesData'	.HermesData .RangedHermesData AnyHermesData AnyHermesData-class HermesData HermesData-class HermesDataFromMatrix RangedHermesData RangedHermesData-class
Inner Joining a Genes with a CDISC Data Set	inner_join_cdisc
Checking for Empty 'SummarizedExperiment'	isEmpty isEmpty,SummarizedExperiment-method
'lapply' method for 'MultiAssayExperiment'	lapply lapply,MultiAssayExperiment-method
Metadata Accessor and Setter	metadata
Example 'MultiAssayExperiment' Data	multi_assay_experiment
Normalization of 'AnyHermesData' Objects	h_cpm h_rlog h_rpkm h_tpm h_voom h_vst normalize normalize,AnyHermesData-method
Prefix Accessor	prefix
Query Gene Annotations from a Connection	query query,character,ConnectionBiomart-method
Row Binding of 'AnyHermesData' Objects	rbind
Renaming Contents of 'SummarizedExperiment' Objects	rename rename,data.frame-method rename,SummarizedExperiment-method
Sample IDs Accessor	samples samples,AnyHermesData-method
Set Technical Failure Flags	set_tech_failure
Show Method for 'AnyHermesData' Objects	show show,HermesData-method show,RangedHermesData-method
Subsetting 'AnyHermesData' Objects	subset
Example 'SummarizedExperiment' Data	summarized_experiment
Summary Method for 'AnyHermesData' Objects	.HermesDataSummary HermesDataSummary HermesDataSummary-class show,HermesDataSummary-method summary summary,AnyHermesData-method
Derivation of Top Genes	.HermesDataTopGenes autoplot,HermesDataTopGenes-method HermesDataTopGenes HermesDataTopGenes-class top_genes
Internal Helper Functions for Validation of 'AnyHermesData' Objects	validate validate_cols validate_col_data validate_counts validate_names validate_prefix validate_row_data
Wrap in MAE	wrap_in_mae

Package: hermes 1.7.2

hermes: Preprocessing, analyzing, and reporting of RNA-seq data

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