openvax pyensembl issues

openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Apache License 2.0

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issues

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Ensembl - Release 85

#161 ericloud closed 8 years ago
3
get_coordinates_from_exon_id() <enhancement>

#160 alec-djinn closed 8 years ago
5
Add gene name aliases

#159 tavinathanson opened 8 years ago
1
WIP: Testing builds within Docker images

#158 armish closed 8 years ago
7
Optimize Travis builds for pyensembl and other pygenomics tools

#157 armish opened 8 years ago
0
Override cache dir if PYENSEMBL_CACHE_DIR is set

#156 armish closed 8 years ago
7
bidirectional_promoter_lncRNA and case sensitivity

#155 joaoe closed 8 years ago
2
Serialization

#154 iskandr closed 8 years ago
11
Added support for Ensembl release 84

#153 iskandr closed 8 years ago
1
Manipulating Gene and Transcript objects.

#152 superDross closed 8 years ago
1
Getting rid of memoization on many properties and methods

#151 iskandr closed 8 years ago
2
Memory Leak / Caching without limits

#150 ryananeff closed 6 years ago
9
moved polymorphic_pseudogene to noncoding biotype group

#149 iskandr closed 8 years ago
4
Missing exon ID column in database for NCBIM37

#148 iskandr closed 6 years ago
3
Nucleotide and protein sequences much larger with Python 2

#147 iskandr closed 8 years ago
0
Added NCBIM37 to list of references for mouse

#146 iskandr closed 8 years ago
5
Specifying install location

#145 rpadmanabhan closed 8 years ago
2
fixed normalize_chromosome, made all_feature_values private

#144 iskandr closed 8 years ago
3
Add documentation to readthedocs

#143 hammer opened 8 years ago
5
Document how to run tests in CONTRIBUTING.md

#142 hammer opened 8 years ago
1
Add Genome.contigs. Fixes #140.

#141 hammer closed 8 years ago
1
Add Genome.contigs()

#140 hammer closed 8 years ago
0
Make Genome.all_feature_values private

#139 hammer closed 8 years ago
1
Add __version__ to pyensembl/__init__.py and parse during build

#138 hammer closed 8 years ago
0
Add pickling for several classes

#137 tavinathanson closed 8 years ago
6
Transcript.coding_sequence didn't work for non-coding transcripts

#136 iskandr closed 8 years ago
1
Fix Ensembl release 83

#135 iskandr closed 8 years ago
1
Increase the max Ensembl version to 83

#134 iskandr closed 8 years ago
1
db attribute error from 'if datacache.db.db_table_exists(db, 'ensembl'):' in database.py

#133 Xerez13 closed 8 years ago
5
Copied new travis config from Varcode

#132 iskandr closed 8 years ago
1
Nose not installed by default

#131 joshim5 opened 8 years ago
2
Added installation of pypandoc to Travis config

#130 iskandr closed 8 years ago
1
+pandoc, -mock

#129 iskandr closed 8 years ago
1
Rename project

#128 hammer opened 9 years ago
8
moved GTF parsing to external gtftools library

#127 iskandr closed 9 years ago
3
Support for satellite ensembl database sites?

#126 xguse opened 9 years ago
4
HGNC Genes

#125 ahmdeen opened 9 years ago
3
Add coveralls to PyEnsembl

#124 tavinathanson closed 9 years ago
1
installation error

#123 tommycarstensen closed 7 years ago
3
Deploy to PyPi on every master commit

#122 tavinathanson closed 9 years ago
1
Add pyensembl build status to README

#121 tavinathanson closed 9 years ago
1
Add unit tests for GTF parsing

#120 iskandr closed 9 years ago
1
Rewrote GTF parsing to use less memory

#119 iskandr closed 9 years ago
5
Stop hammering ensembl.org for GTF/FASTA files

#118 tavinathanson closed 6 years ago
1
Update deprecated skbio functionality to newer equivalnets

#117 iskandr closed 9 years ago
1
Combine path munging between GTF and SequenceData

#116 tavinathanson opened 9 years ago
0
Automatically populate species/release/reference mapping

#115 tavinathanson opened 9 years ago
0
Refactoring to support species in EnsemblRelease and to simplify download/install logic

#114 iskandr closed 9 years ago
10
Many gene synonyms are not recognised by genes_by_name()

#113 alec-djinn opened 9 years ago
4
Load mouse VCF files

#112 iskandr closed 9 years ago
1

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