bigdatagenomics/rice issues and pull requests

#83 - Update ADAM dependency to version 0.23.0.

Pull Request - State: open - Opened by heuermh about 7 years ago - 3 comments

#82 - Changed Index to use Debruijn graphs

Pull Request - State: open - Opened by ananth-pallaseni almost 9 years ago - 1 comment

#81 - Changed Index to use Debruijn graphs

Pull Request - State: closed - Opened by ananth-pallaseni almost 9 years ago - 3 comments

#80 - Provide separate artifacts for scala 2.10/2.11

Issue - State: open - Opened by heuermh over 9 years ago

#79 - Update EM algorithm

Issue - State: open - Opened by fnothaft over 9 years ago

#78 - Allow using aligned reads as input

Issue - State: open - Opened by fnothaft over 9 years ago

#77 - Update indexer to use ananas's colored de Bruijn graph

Issue - State: open - Opened by fnothaft over 9 years ago - 1 comment

#76 - Index works, but is slow

Pull Request - State: closed - Opened by ananth-pallaseni over 9 years ago - 1 comment

#75 - Rename to rice

Pull Request - State: closed - Opened by fnothaft over 9 years ago

#74 - Working Index Metrics

Pull Request - State: closed - Opened by ananth-pallaseni over 9 years ago - 1 comment

#73 - [RNAdam-72] Add instrumentation to RNAdam.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#72 - Reissue of PR #71

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 3 comments

#71 - Fixing bottleneck in Index

Pull Request - State: closed - Opened by ananth-pallaseni almost 10 years ago - 5 comments

#70 - [RNAdam-68] Adds CLI for quantification.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 5 comments

#69 - [RNAdam-67] Branch defuse.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#68 - Add back CLI

Issue - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#67 - Move Defuse into a branch

Issue - State: closed - Opened by fnothaft almost 10 years ago

#66 - Added Index in Quantification along with tests

Pull Request - State: closed - Opened by ananth-pallaseni almost 10 years ago - 8 comments

#65 - Fixing build issue due to context removal in region join.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#64 - [RNAdam-53] Calibrate the transcript isoform abundances for transcript length bias.

Pull Request - State: closed - Opened by niranjan93 almost 10 years ago - 7 comments

#63 - [RNAdam-63] Remove reference mapping context.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#62 - [RNAdam-62] Upgrade ADAM and bdg-utils dependencies.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#61 - [RNAdam-60] Remove non-ADAMContext *Context references.

Pull Request - State: closed - Opened by fnothaft almost 10 years ago - 1 comment

#60 - Remove *Context References

Issue - State: closed - Opened by fnothaft almost 10 years ago

#59 - [RNAdam-58] Upgrade to ADAM 0.15.1-SNAPSHOT

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 1 comment

#58 - Upgrade to ADAM 0.15.1-SNAPSHOT

Issue - State: closed - Opened by fnothaft about 10 years ago
Labels: enhancement

#57 - any docs

Issue - State: open - Opened by antonkulaga about 10 years ago - 1 comment

#56 - Add regression based technique for calibrating k-mer counts

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 20 comments

#55 - Support clustering for expression data

Issue - State: open - Opened by fnothaft about 10 years ago
Labels: enhancement, quantification

#54 - Calibrate k-mer counts vs. sequence context

Issue - State: closed - Opened by fnothaft about 10 years ago
Labels: enhancement, quantification

#53 - Normalize abundance by transcript length

Issue - State: closed - Opened by fnothaft about 10 years ago - 1 comment
Labels: enhancement, quantification

#52 - [RNAdam-50] Add more realistic transcript simulator.

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 6 comments

#52 - [RNAdam-50] Add more realistic transcript simulator.

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 6 comments

#51 - Modification to EM algorithm

Pull Request - State: closed - Opened by niranjan93 about 10 years ago - 6 comments

#50 - Add tests for non-independent transcripts

Issue - State: closed - Opened by fnothaft about 10 years ago
Labels: enhancement, quantification

#49 - Adds simple read simulator

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 7 comments

#48 - Add simulator for Quantify unit tests

Issue - State: closed - Opened by fnothaft about 10 years ago
Labels: enhancement

#47 - [RNAdam-33] Implements EM algorithm used in Sailfish transcript quantification.

Pull Request - State: closed - Opened by niranjan93 about 10 years ago - 5 comments

#46 - Collect transcript lengths prior to EM

Pull Request - State: closed - Opened by fnothaft about 10 years ago - 4 comments

#45 - Collect transcript lengths

Issue - State: closed - Opened by fnothaft about 10 years ago
Labels: enhancement

#44 - [RNAdam - 32] Added EM initialization code.

Pull Request - State: closed - Opened by niranjan93 over 10 years ago - 5 comments

#43 - [RNAdam-42] Remove sequence dictionary from region join

Pull Request - State: closed - Opened by fnothaft over 10 years ago - 3 comments

#42 - Remove sequence dictionary from region join

Issue - State: closed - Opened by fnothaft over 10 years ago
Labels: bug

#41 - Added joinTranscripts in Quantify

Pull Request - State: closed - Opened by ananth-pallaseni over 10 years ago - 7 comments

#40 - Upgrading to downstream updates in ADAM

Pull Request - State: closed - Opened by fnothaft over 10 years ago - 2 comments

#39 - Remove Gene models

Issue - State: closed - Opened by fnothaft over 10 years ago - 1 comment
Labels: enhancement

#38 - Fix broken build due to upstream changes

Issue - State: closed - Opened by fnothaft over 10 years ago
Labels: bug

#37 - Implemented the mapKmersToClasses method in Quantify.scala

Pull Request - State: closed - Opened by niranjan93 over 10 years ago - 6 comments

#36 - [RNAdam-35] Upgrades to ADAM 0.14.1-SNAPSHOT.

Pull Request - State: closed - Opened by fnothaft over 10 years ago - 3 comments

#35 - Move to ADAM 0.14.1-SNAPSHOT

Issue - State: closed - Opened by fnothaft over 10 years ago