MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data.On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.

Citation

If you use MERFISHtools, please cite our paper

Köster, Johannes, Myles Brown, X. Shirley Liu. “A Bayesian Model for Single Cell Transcript Expression Analysis on MERFISH Data.” Bioinformatics 2018. https://doi.org/10.1093/bioinformatics/bty718.

Installation

MERFISHtools can be installed and updated easily viaBioconda.

Usage

For usage instructions at the command line, please issue

merfishtools --help

A typical MERFISHtools workflow is as follows.

Step 1: Estimate transcript expressions

Transcript expressions are estimated from raw MERFISH data via

merfishtools exp --threads 8 codebook.txt data.txt --estimate estimates.txt > expression.txt

See

merfishtools exp --help

for additional parameters.

Input

The filecodebook.txt is a MERFISH codebook (example), consisting of tab separated columns:

• feature,
• codeword
• expressed.

The last column has to contain a 1 if a feature is expressed (e.g. it is a transcript or gene), and a 0 if it is a misidentification probe (see Chen et al. Science 2015). Note that these probes are important for MERFISHtools to estimate noise rates and provide more accurate predictions.

The filedata.txt (example) contains MERFISH readouts in tab-separated format. The expected columns are

• cell,
• feature,
• hamming_dist,
• cell_position_x,
• cell_position_y,
• rna_position_x,
• rna_position_y.

When using MERFISH protocol v2, you will have a binary file format containing the readouts. Merfishtools will detect this automatically.

Output

Results are provided as probability mass functions (PMF) at STDOUT, in the format

• cell,
• feature (e.g. gene, transcript),
• expression,
• posterior probability.

Further, the optional flag--estimate estimates.txt results in a table with expression estimates of the form:

• cell,
• feature,
• maximum a posteriori (MAP) estimate,
• standard deviation,
• maximum a-posteriori probability estimate (MAP),
• lower bound of 95% credible interval,
• upper bound of 95% credible interval.

Step 2: Estimate differential expression

Two conditions

In case of two conditions, you can issue

merfishtools diffexp --threads 8 expression1.txt expression2.txt > diffexp.txt

to calculate differentially expressed transcripts.See

merfishtools diffexp --help

for additional parameters.

Input

The filesexpression1.txt andexpression2.txt (example) contain the PMFs of the two conditions to compare, and are obtained by running step 1 on the data for each condition.

Output

Results are provided as tab separated table at STDOUT (here piped into the filediffexp.txt) with columns

• feature (e.g. gene, transcript),
• posterior error probability (PEP) for differential expression,
• expected FDR when selecting all features down to the current,
• bayes factor (BF) for differential expression,
• maximum a posteriori (MAP) log2 fold change of first vs second group,
• standard deviation of log2 fold change,
• maximum a posteriori (MAP) log2 fold change,
• lower bound of 95% credible interval of log2 fold change,
• upper bound of 95% credible interval of log2 fold change.

Multiple conditions

In case of more than two conditions, you can issue

merfishtools multidiffexp --threads 8 expression1.txt expression2.txt expression3.txt ... > diffexp.txt

to calculate differentially expressed transcripts. Here, the coefficient of variation over the condition means is used as measure for differential expression. See

merfishtools multidiffexp --help

for additional parameters.

Input

The filesexpression1.txt andexpression2.txt, … (example) contain the PMFs of the conditions to compare, and are obtained by running step 1 on the data for each condition.

Output

Results are provided as tab separated table at STDOUT (here piped into the filediffexp.txt) with columns

• feature (e.g. gene, transcript),
• posterior error probability (PEP) for differential expression,
• expected FDR when selecting all features down to the current,
• bayes factor (BF) for differential expression,
• maximum a posteriori (MAP) coefficient of variation (CV),
• standard deviation of CV,
• maximum a posteriori (MAP) CV,
• lower bound of 95% credible interval of CV,
• upper bound of 95% credible interval of CV.

Author

Johannes Köster

License

MIT