hammerlab immuno issues

hammerlab / immuno

Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)

Apache License 2.0

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fatal error when use vcf file

#173 serge2016 closed 8 years ago
1
from immuno.mutate import ( ImportError: No module named immuno.mutate

#172 serge2016 opened 8 years ago
0
Use thymic deletion self filter for peptide lengths other than 9

#171 iskandr opened 9 years ago
1
Invalid URL for IEDB's MHC web API

#170 iskandr opened 9 years ago
0
More logging for already seen sequences

#169 tavinathanson closed 9 years ago
1
Only use most abundant isoform for each gene

#168 iskandr opened 9 years ago
0
Replace FASTA input to mutation_report with a script for analyzing viral proteomes

#167 iskandr opened 9 years ago
0
Make separate project for web frontend

#166 iskandr opened 9 years ago
0
Replace epitope/peptide dictionaries with objects or namedtuples

#165 iskandr opened 10 years ago
0
split apart dependencies of vaccine peptide selection

#164 iskandr closed 9 years ago
2
Download a file that maps from transcript ID to name, and use that in the viz

#163 tavinathanson closed 10 years ago
0
Show empty ref/alt nucleotides with dash

#162 iskandr opened 10 years ago
0
Adding a dummy RNA expression upload

#161 tavinathanson closed 10 years ago
0
Adding pan/cons/random choices for the web app

#160 tavinathanson closed 10 years ago
0
Use d3's mouse method to get x coordinate

#159 tavinathanson closed 10 years ago
1
Columnize viz

#158 tavinathanson closed 10 years ago
0
Web UI: adding a patient isn't transactional

#157 iskandr closed 10 years ago
1
Document dependencies for web frontend

#156 iskandr opened 10 years ago
0
Add error checking/asserts to peptides.js

#155 tavinathanson opened 10 years ago
0
Remove old table CSS and use bootstrap for table styling

#154 tavinathanson closed 10 years ago
0
Adding the notion of stored output via the Run object

#153 tavinathanson closed 10 years ago
0
Weird patient names can cause URL issues

#152 tavinathanson opened 10 years ago
0
A patient named "new" will cause issues

#151 tavinathanson opened 10 years ago
0
Adding flash messages for file upload, and removed an unnecessary route

#150 tavinathanson closed 10 years ago
0
Add basic bootstrap styling to make immuno look not-awful

#149 tavinathanson closed 10 years ago
0
Adding chr/pos/etc. to the visualization

#148 tavinathanson closed 10 years ago
0
Setting the Biomart query to Ensembl 75

#147 tavinathanson closed 10 years ago
2
Link epitopes viz

#146 tavinathanson closed 10 years ago
1
Link together /profile, /patient/new, and /patient/name

#145 tavinathanson closed 10 years ago
3
Basic file uploading

#144 tavinathanson closed 10 years ago
2
Added sign in and registration using SQLAlchemy and Flask-User

#143 tavinathanson closed 10 years ago
4
printing rows of VCF dataframe as table in template

#142 iskandr closed 10 years ago
0
Changing arg parsing to env variables

#141 tavinathanson closed 10 years ago
1
Adding CSS and templates for the basic Flask app

#140 tavinathanson closed 10 years ago
1
Adding CSS and templates to the basic Flask app

#139 tavinathanson closed 10 years ago
2
print VCF dataframe on UI

#138 iskandr closed 10 years ago
1
Adding the most basic Flask file for a UI

#137 tavinathanson closed 10 years ago
1
remove trailing whitespace, other formatting

#136 iskandr closed 10 years ago
0
added TCGA unit tests, moved test data to subdirectory, added forgotten ...

#135 iskandr closed 10 years ago
1
Use a different temp directory for each NetMHCcons instance, moved

#134 iskandr closed 10 years ago
2
Add capability to group transcripts by gene name

#133 tavinathanson opened 10 years ago
0
Investigate get_transcript_index_from_pos in annotation

#132 tavinathanson opened 10 years ago
0
launch multiple netmhccons processes simultaneously

#131 iskandr closed 10 years ago
0
make analyze_cohort resumable and prevent NetMHCcons from crashing when ...

#130 iskandr closed 10 years ago
0
Added support for MHC binding prediction via local copy of NetMHCcons

#129 iskandr closed 10 years ago
0
parse TAB variant files, changed some commandline flags

#128 iskandr closed 10 years ago
2
Adding .travis.yml to integrate with Travis CI, as well as an associated...

#127 tavinathanson closed 10 years ago
1
First attempt at getting Travis CI to work with immuno

#126 tavinathanson closed 10 years ago
3
Added gene expression filtering using RNASeq data

#125 tavinathanson closed 10 years ago
2
Fix for non-transcript IDs by adding proper column headers. Closes #123.

#124 tavinathanson closed 10 years ago
1