array_fitting_tools

add to python path: array_fitting_tools/bin

Requirements (parantheses indicate what I am using):

Please update this list as you encounter dependencies not listed here!

pandas (0.16.2)
lmfit (0.8.3) ** Note that lmfit 0.9.0+ would NOT work with the current pipeline.
joblib (0.9.0b2)
seaborn (0.7.0)
scikits.bootstrap (0.3.2)
statsmodels (0.6.1)
scipy (0.16.0)
numpy (1.11.1)

findSeqDistribution to annotate variants onto clusters.

processData to make series file from CPfluor directories.
normalizeSeries to normalize fluoresecence by all-cluster images.
singleClusterFits to do initial, minimally constrained fits on all single clusters.
findFmaxDist to fit the distribution of fmax of good variants.
bootStrapFits to revise estimates by constraining fmax and bootstrapping the fits.

processData to make series file from CPfluor directories.
normalizeSeries to normalize fluoresecence by all-cluster images.
fitRatesPerCluster to fit individual clusters to on/off rates.
bootStrapFitFile to bootstrap fit parameter to obtain 95% confidence intervals.

run_all_binding_curves.sh can be used to run all 4 scripts.
compressBarcodes can take in a CPseq file and find unique barcode file. Also assesses quality.
fitBackgroundTile will fit background clusters with the same method used above to better understand how noise contributes to fit values
- This one probably won't work out of the box: talk to me.
medianSubsetCPseries will take the per-variant median of a CPseries, and optionally subset to only include one tile.

For more info, see the wiki page