Ship emissions are important contributor to air pollution and the climate through interacting with clouds. They are the dominant anthropogenic source over the oceans. However, their magnitudes still have large uncertainty. Here we develop a deep learning model to detect ship-emitted NO2 plumes at the pixel level in TROPOMI tropospheric NO2 data. The trained model performs well and, when applied to a year of data, it finds major shipping routes, but misses several other routes. We show that high cloudiness in these shipping routes is the culprit because clouds block signals from reach the sensor. Indeed, detected shipping routes in this study complements shipping routes detected using ship-tracks that is only available in cloudy regions. Our method can find application in several areas such as improving ship emission estimates and compliance verifications. Our method will benefit from improved tropospheric NO2 retrievals since their quality is critical for plume detection.