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openvax
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pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Get rid of ensembl id validation
#211
iskandr
closed
6 years ago
1
added exception is_valid_id for yeast
#210
rraadd88
closed
6 years ago
2
Add an exception for Saccharomyces cerevisiae in `is_valid_ensembl_id(ensembl_id)` function
#209
rraadd88
closed
6 years ago
0
Upload new versions to both PyPI and bioconda
#208
iskandr
opened
6 years ago
1
Species not found error
#207
a-jacobo
closed
9 months ago
13
try installing Ensembl data from github
#206
iskandr
closed
6 years ago
0
List dirs in cli
#205
iskandr
closed
6 years ago
0
Can not install species anymore
#204
nnekaede
closed
6 years ago
2
try not using trusty
#203
iskandr
closed
6 years ago
0
Name of ENSG00000275303 missing from Ensembl 80
#202
iskandr
opened
6 years ago
0
Download from ftp.ensembl.org fails on Travis
#201
iskandr
closed
6 years ago
1
exception running basic pyensembl install command
#200
ghost
closed
6 years ago
7
Crash during install (pyanddoc not installed)
#199
joaoe
closed
6 years ago
3
Restrict which GTF columns are loaded to speed up database construction
#198
iskandr
closed
6 years ago
0
More Travis updates
#197
julia326
closed
6 years ago
1
Fixing travis
#196
iskandr
closed
6 years ago
5
Installing Ensembl release fails at reading GTF step
#195
maximz
closed
6 years ago
7
Is it possible to download a set of reference genomes (bacterial, fasta) by e.g. their assembly ID?
#194
phiweger
opened
6 years ago
1
Can't retrieve transcript's sequence from a FASTA file
#193
vnvkotova
opened
6 years ago
2
PyEnsembl breaks Travis by running out of disk space
#192
iskandr
closed
6 years ago
0
Don't require users to download latest Ensembl every time we bump the MAX_ENSEMBL_RELEASE
#191
iskandr
closed
6 years ago
0
Union of gene intervals
#190
willgdjones
opened
7 years ago
0
data install location vs cache location
#189
0xaf1f
opened
7 years ago
3
Downloading more recent Ensembl releases E.g: 90
#188
vmkalbskopf
closed
6 years ago
2
PDB IDs from gene_ids?
#187
tommycarstensen
closed
7 years ago
2
Support something like bedtools intersect
#186
tavinathanson
opened
7 years ago
0
Add non-coding RNA sequences to pyensembl
#185
murphycj
closed
7 years ago
19
Add sequence attribute to non-coding transcripts
#184
murphycj
closed
7 years ago
9
Add rat, dog, cat, chicken species & increase MAX_ENSEMBL_RELEASE to 87
#183
iskandr
closed
7 years ago
2
non-human or mouse species
#182
JoseBlanca
closed
7 years ago
5
Non-Ensembl GTF
#181
lidiaiprou
opened
7 years ago
1
Support hg19
#180
ihodes
opened
7 years ago
2
added caching to dir containing Ensembl downloads and database/indices
#179
iskandr
closed
7 years ago
4
fix typo in shell help message
#178
neoflex
closed
7 years ago
2
Add biotype argument to transcripts()
#177
iskandr
opened
7 years ago
0
coding_sequence_position_ranges and coding_sequence don't agree
#176
gshiba
opened
7 years ago
3
err fixing number typo in RELEASING.md instructions
#175
julia326
closed
7 years ago
4
Fix logging file access in shell (needed pkg_resources)
#174
julia326
closed
7 years ago
3
Stable Ensembl ID
#173
erichu8
opened
7 years ago
5
Add a RELEASING.md
#172
julia326
closed
7 years ago
0
one logger per module
#171
julia326
closed
7 years ago
7
One logger per module
#170
julia326
closed
7 years ago
0
Support all protein coding biotypes
#169
joaoe
opened
8 years ago
2
Compatability with Gencode GTF
#168
GuyAllard
opened
8 years ago
2
Configurable cache location
#167
joaoe
closed
8 years ago
5
Added protein coding biotype tests
#166
iskandr
closed
8 years ago
2
Got rid of biotypes.py
#165
iskandr
closed
8 years ago
5
Generalize deserialization caching
#164
tavinathanson
closed
6 years ago
1
Deserialization should construct cached EnsemblRelease objects
#163
iskandr
closed
8 years ago
6
Ensembl release 85
#162
iskandr
closed
8 years ago
1
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