Man pages for almeidasilvaf/bear
Building Expression Atlas from RNA-Seq data
| check_md5 | Check file integrity with md5sum |
| create_dir_structure | Create a standard directory for bears |
| create_sample_info | Search the SRA database and create a data frame of sample... |
| download_from_ena | Download FASTQ files from ENA's FTP |
| fastp_is_installed | Check if fastp is installed |
| fastq_exists | Check if FASTQ files were properly downloaded |
| featureCounts | Count reads with featureCounts |
| featureCounts2se | Create a SummarizedExperiment object from featureCounts... |
| get_url_ena | Get URL for each file in the ENA's FTP repository |
| gff2bed | Convert GFF file to BED |
| infer_strandedness | Infer library strandedness |
| kallisto2se | Create a SummarizedExperiment object from kallisto output |
| kallisto_index | Index the transcriptome for kallisto |
| kallisto_is_installed | Check if kallisto is installed |
| kallisto_quantify | Quantify expression with kallisto |
| mapping_pass | Keep only samples that passed minimum requirements in STAR... |
| mapping_qc | Summary statistics of STAR mapping QC |
| multiqc_is_installed | Check if multiqc is installed |
| remove_rrna | Remove rRNA sequences from .fastq files with SortMeRNA |
| rseqc_is_installed | Check if RSeQC is installed |
| salmon2se | Create a SummarizedExperiment object from salmon output |
| salmon_index | Index the transcriptome for salmon |
| salmon_is_installed | Check if salmon is installed |
| salmon_quantify | Quantify expression with salmon |
| sample_info | Sample metadata |
| sortmerna_is_installed | Check if SortMeRNA is installed |
| star_align | Align reads to a reference genome using STAR |
| star_genome_index | Index genome for STAR alignment |
| star_is_installed | Check if STAR is installed |
| stringtie2se | Create a SummarizedExperiment object from StringTie output |
| stringtie_assemble | Assemble transcripts with StringTie |
| stringtie_is_installed | Check if StringTie is installed |
| stringtie_quantify | Quantify expression in TPM with StringTie |
| subread_is_installed | Check if subread is installed |
| summary_stats_fastp | Get read quality summary statistics from fastp |
| summary_stats_salmon | Get salmon mapping rate for each BioSample |
| summary_stats_star | Get mapping summary statistics from STAR |
| taco_is_installed | Check if TACO is installed |
| taco_merge | Merge assembled transcripts with TACO |
| translate_strandedness | Translate library orientation terminology for each program |
| trim_reads | Trim low-quality bases and adapters using fastp |
| tx2gene | Transcript to gene mapping |
