# Putting the fun in LINCS L1000 data analysis

## Documentation for package ‘slinky’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.zs | .zs
chDir | chDir
close | closeAll
closeAll | closeAll
closeAll-method | closeAll
clue | clue
clue-method | clue
clueCount | clueCount
clueCount-method | clueCount
clueInstances | clueInstances
clueInstances-method | clueInstances
clueVehicle | clueVehicle
clueVehicle-method | clueVehicle
coerce | as("Slinky", "SummarizedExperiment")
coerce-method | as("Slinky", "SummarizedExperiment")
colnames | colnames
colnames-method | colnames
controls | controls #' Fetch the same plate control samples applicable for given ids (distil_id). Expects that the specified ids have pert_type of trt_sh or trt_cp.
controls-method | controls #' Fetch the same plate control samples applicable for given ids (distil_id). Expects that the specified ids have pert_type of trt_sh or trt_cp.
diffexp | diffexp
diffexp-method | diffexp
download | download
download-method | download
ks | ks
loadL1K | loadL1K
loadL1K-method | loadL1K
metadata | metadata
metadata-method | metadata
ncol | Slinky object dimensions
ncol-method | Slinky object dimensions
nrow | Slinky object dimensions
nrow-method | Slinky object dimensions
readGCTX | readGCTX
readGCTX-method | readGCTX
rownames | rownames
rownames-method | rownames
rzs | rzs
rzs-method | rzs
Slinky | An S4 class for working with LINCS data
Slinky-class | An S4 class for working with LINCS data
[-method | Subsetting Slinky objects