HTSeq for high through put sequencing data
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
Cogent
https://pypi.python.org/pypi/cogent
pygr
http://code.google.com/p/pygr/
pybedtools
http://pythonhosted.org/pybedtools/
TAMO for motif analysis
http://fraenkel.mit.edu/TAMO/TAMO_tutorial.html
Biopython
https://pypi.python.org/pypi/biopython/1.61
cruzdb
https://pypi.python.org/pypi/cruzdb/0.4
This blog by Tommy Tang is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
update:
ReplyDeletehttps://github.com/chapmanb/bcbio-nextgen
bx-python https://bitbucket.org/james_taylor/b...pts?at=default
metaseq http://pythonhosted.org/metaseq/
MISO http://genes.mit.edu/burgelab/miso/docs/index.html
Nesoni for RNA-seq http://www.vicbioinformatics.com/nesoni-cookbook/#
reditools https://code.google.com/p/reditools/
blacktie for RNA-seq http://blacktie.readthedocs.org/en/latest/