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psathyrella
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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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Improve upon hierarchical agglomeration
#178
psathyrella
closed
6 years ago
0
Implicit info warnings
#177
Irrationone
closed
8 years ago
5
Average naive hfrac over N best naive sequences
#176
psathyrella
opened
8 years ago
2
Investigate potential for using shared mutations for clustering
#175
matsen
opened
8 years ago
2
Multiple replicates as input?
#174
matsen
opened
8 years ago
0
add samtools version check
#173
psathyrella
closed
8 years ago
1
Use a heuristically built tree to reduce logprob calculations?
#172
matsen
opened
8 years ago
0
Figure out relationship between sequences that logprob and naive hfrac get right/wrong
#171
psathyrella
closed
7 years ago
1
See how much it helps to recalculate a logprob if it's for different kbounds
#170
psathyrella
closed
8 years ago
2
Reduce n_procs in sw for iterations after the first
#169
psathyrella
closed
8 years ago
0
Minimize number of states in each loop
#168
psathyrella
closed
8 years ago
4
Improve simulation of very highly mutated sequences
#167
psathyrella
closed
3 years ago
0
Ghost states?
#166
psathyrella
closed
7 years ago
1
Improve full-repertoire reconstruction on large samples
#165
psathyrella
opened
8 years ago
2
Work up a web interface
#164
psathyrella
opened
8 years ago
8
Write nonsense annotations to output, but skip them internally
#163
psathyrella
closed
8 years ago
0
Don't run multi HMM on all the seqs in a big cluster
#162
psathyrella
closed
8 years ago
5
Aligned d and j columns too, please!
#161
matsen
closed
8 years ago
0
Memory optimizations
#160
psathyrella
opened
8 years ago
1
Bayesian estimation of parameters when data is weak
#159
matsen
closed
8 years ago
1
Set vsearch n_procs properly
#158
psathyrella
closed
8 years ago
1
Test double indels
#157
psathyrella
closed
7 years ago
0
Test caching with and without naive_hfracs
#156
psathyrella
closed
8 years ago
1
switch ham cacheing back to keying on query names instead of sequences
#155
psathyrella
closed
8 years ago
0
Cache smith-waterman results
#154
psathyrella
closed
8 years ago
0
handle paired heavy and light chain data
#153
psathyrella
closed
3 years ago
11
Fix compilation things from Jakub
#152
psathyrella
closed
8 years ago
3
Reduce memory usage
#151
psathyrella
closed
8 years ago
1
How do we want to tell users to handle batch parallelization?
#150
psathyrella
closed
8 years ago
9
add indelfo to output csv
#149
psathyrella
closed
8 years ago
0
streamline clusterpath::write_partitions
#148
psathyrella
closed
8 years ago
0
Check how heuristic thresholds depend on sequence length
#147
psathyrella
closed
8 years ago
2
Clean up query divvy code
#146
psathyrella
closed
8 years ago
0
make sure padding info, indel info, and read truncation are playing nicely with each other
#145
psathyrella
closed
8 years ago
0
Add better performance metrics to `scons test`
#144
psathyrella
closed
8 years ago
1
track down bad conserved codon errors in simulator
#143
psathyrella
closed
8 years ago
1
fix up simulation parallization
#142
psathyrella
closed
8 years ago
0
Start tagging versions
#141
psathyrella
closed
8 years ago
1
clean naive hamming treatment and bcrham
#140
psathyrella
closed
8 years ago
0
Test how well tigger works for identifying new alleles
#139
psathyrella
closed
8 years ago
1
Speed up git
#138
psathyrella
closed
8 years ago
3
Blue sky improvements
#137
psathyrella
closed
8 years ago
1
Reconstruct only the N largest clonal families
#136
psathyrella
closed
7 years ago
2
make ROCs for naive hamming vs log prob ratio
#135
psathyrella
closed
8 years ago
0
are log probs getting cached with both orderings?
#134
psathyrella
closed
9 years ago
1
clean up indel code
#133
psathyrella
closed
8 years ago
0
Run on people's data
#132
psathyrella
closed
8 years ago
1
Try harder to equalize the number of forward calculations over all processes
#131
psathyrella
closed
8 years ago
0
clean up/update no valid path error message
#130
psathyrella
closed
8 years ago
0
Decide whether to print or not print extra N padding in annotation output
#129
psathyrella
closed
8 years ago
0
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