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Function: Prepare transcript references for RSEM and optionally build BOWTIE/BOWTIE2/STAR indices.
Usage: rsem-prepare-reference [options] reference_fasta_file(s) reference_name
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Function: Impute representative cell type-specific expression profiles
Usage: docker run <bind_mounts> cibersortx/gep [options] --mixture <file> --sigmatrix <file>
Supported input format:
TSV, TXT
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Function: Impute high resolution cell type-specific expression from bulk genomic profiles
Usage: docker run <bind_mounts> cibersortx/hires [options] --mixture <file> --sigmatrix <file>
Supported input format:
TSV, TXT
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Function: Perform dual-phase, selective-alignment-based estimation of transcript abundance from RNA-seq reads
Usage: salmon quant [options] -t transcripts.fa -l <LIBTYPE> -a aln.bam -o salmon_quant
Supported input format:
BAM
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Function: Make a RSEM compatible BAM file
Usage: convert-sam-for-rsem [options] <input.sam/input.bam/input.cram> output_file_name
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Function: Check if the SAM/BAM file satisfy RSEM's requirements.
Usage: rsem-sam-validator <input.sam/input.bam/input.cram>