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psathyrella
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partis
B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction
GNU General Public License v3.0
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Support TCRs
#228
laserson
closed
7 years ago
6
Handle with multiple annotations
#227
bernste1
closed
6 years ago
1
Should we handle VDDJ rearrangements?
#226
psathyrella
opened
7 years ago
4
Indels at near beginning of sequence (FR1-FR2) not being removed
#225
Irrationone
closed
6 years ago
32
Using partis to trim NGS reads
#224
krdav
closed
7 years ago
4
add warning flags to ig-sw
#223
psathyrella
closed
7 years ago
1
installation on CentOS
#222
HaiaK
closed
6 years ago
13
Read count tracking
#221
Irrationone
closed
7 years ago
5
Nonsense k bounds exception
#220
Irrationone
closed
6 years ago
7
Multi-samples data
#219
Irrationone
closed
6 years ago
13
Output more S-W details for linearham
#218
matsen
closed
6 years ago
19
Light chain partitioning inconsistencies
#217
krdav
closed
7 years ago
3
Clarifying the annotations from partitioning
#216
krdav
closed
7 years ago
1
cdr3_length in light chain samples
#215
krdav
closed
7 years ago
6
Warnings after adding custom germline database
#214
krdav
closed
7 years ago
10
Header name error
#213
Irrationone
closed
7 years ago
3
Unequal sequence length exception
#212
Irrationone
closed
7 years ago
21
fix ig-sw cigar query length mismatch
#211
psathyrella
closed
6 years ago
12
Allel finding continues finding more and more allels
#210
krdav
closed
7 years ago
2
Option of both lambda and kappa option for light chain annotation
#209
krdav
closed
7 years ago
2
Not reproducible results after VL update
#208
krdav
closed
8 years ago
5
SW alignment slow down in newer version
#207
krdav
closed
8 years ago
2
use base quality scores in allele finding
#206
psathyrella
closed
4 years ago
1
Apparent allele detection bug
#205
scharch
closed
8 years ago
2
Add non-human flag
#204
psathyrella
closed
8 years ago
6
Decide how to fail when trying to cache parameters on very few sequences
#203
psathyrella
closed
8 years ago
1
Filter out/replace forbidden characters (:;,) rather than forbidding them
#202
psathyrella
closed
7 years ago
0
Cannot simulate more than 50 sim-events
#201
fdtomasi
closed
8 years ago
1
ig-sw
#200
apurvaraman
closed
8 years ago
2
stops in inferred naive sequence
#199
jotwin
closed
6 years ago
9
Add mutation freq to output csv
#198
psathyrella
closed
8 years ago
0
in frame and stops correct?
#197
jotwin
closed
8 years ago
10
Allow to use annotation output file as input for partitioning
#196
psathyrella
closed
5 years ago
7
cdr3 info in annotation output
#195
jotwin
closed
8 years ago
3
Big difference in length found in same partition
#194
krdav
closed
6 years ago
10
machine learning for automatic heuristics
#193
matsen
opened
8 years ago
3
Exorbitantly high memory usage during full/naive hamming partitioning
#192
krdav
closed
6 years ago
16
remove boost dependency
#191
psathyrella
closed
7 years ago
3
Parallelization on other queueing systems
#190
krdav
closed
7 years ago
19
add emissions rescaling to bcrham scons test
#189
psathyrella
opened
8 years ago
0
Run fail on torque queuing system because of "stty size" command
#188
krdav
closed
8 years ago
2
Exception: couldn't find calcd line....
#187
krdav
closed
8 years ago
4
Add tree information to simulation output
#186
psathyrella
closed
5 years ago
1
"which: no srun in $PATH"
#185
namita1025
closed
8 years ago
0
--infname missing
#184
namita1025
closed
8 years ago
0
package import paths
#183
namita1025
closed
8 years ago
1
Swap per_gene_support delimiters
#182
namita1025
closed
8 years ago
1
turn --actions into subparsers
#181
psathyrella
closed
8 years ago
2
Documentation for generate_trees
#180
Irrationone
closed
8 years ago
5
Wean erick off partis alignments
#179
psathyrella
closed
7 years ago
0
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