Releases: molgenis/systemsgenetics
Releases · molgenis/systemsgenetics
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Merge pull request #542 from PatrickDeelen/master Version bump to make release
Systems Genetics 1.4.0_18-11.1
Merge pull request #514 from PatrickDeelen/master Lot of stuff. Mostly genenetwork
Systems Genetics v1.0.2
Changes since v1.0.1
| Pull request | Description |
|---|---|
| #444 | Adding full stop in integer/float lists to denote missing values |
| #442 | Upgrade Apache Commons Collections to v3.2.2 |
| #440 | Long overdue merge |
| #439 | Add headers, minimum reads option to CTSASE |
| #435 | update risk scores |
| #434 | An addition of plotting and negative cell type specific effects |
| #433 | Fix build |
| #432 | Pull request to fix small bugs, based on likelihood compared to log likelihood, renamed to covariate specific allele specific expression, changed the pom to add Covariate specific ASE. |
| #431 | Switch to older version parallel colt |
| #430 | Fixes to Java PCoA tool |
| #429 | POM fix |
| #428 | Long over due merge |
| #427 | Add test and gene region in the ASEperRegion and add to the Wiki |
| #426 | Interaction analysis: added an option to skip covariate normalization |
| #425 | Interaction stuff |
| #424 | samtools index output to .bam.bai instead of .bam.idx |
| #423 | add example genotypeHarmonizer tritype conversion |
| #422 | removed some small errors and inconsistencies in README and removed an old folder. |
| #421 | add cell type specific ASE to systems genetics |
| #417 | Interaction stuff |
| #416 | Fix2 |
| #415 | Possible jenkins fix |
| #413 | added an option to set the number of threads |
| #412 | Last steps interaction software including file writer for skipped interactions |
| #411 | Interaction stuff |
| #410 | Skip interaction analysis for covariates affected by eSNPs |
| #409 | Option to test specific covariates |
| #408 | All kind of interaction stuff |
| #407 | Clean up and interaction stuff |
| #406 | added an option for running permutations |
| #405 | All kind of interaction stuff |
| #404 | small bug fixes in Lude's interaction analysis |
| #403 | no eQTL confinement case fixed + minor edits |
| #402 | merge with dasha |
| #401 | Added options and gene distance check to Lude's interaction analysis |
| #399 | All kind of interaction stuff |
| #398 | added testing specific eQTLs Lude's interaction analysis |
| #397 | Regress out covariates |
| #396 | Fix? |
| #395 | Lude interaction analysis + some minor stuff |
| #394 | Speed-up for QN and other ranking with tie |
| #393 | HiC annotation |
| #392 | Plink chr names and minor stuff |
| #390 | Small changes, bump version meta-analyzer |
| #389 | BinMeta fixes |
| #388 | Interaction stuff + version bump |
| #387 | fix results buffer binaryMeta |
| #386 | removed debug souts and added snapshot |
| #385 | fixes |
| #384 | Interaction analysis edits |
| #383 | Some more minor edits |
| #382 | Update InteractionAnalysisMultiThreaded.java |
| #380 | Fix lavaan, update POM to include new genetica libraries, other edits |
| #379 | Fix double matrix dataset + some interaction stuff |
| #378 | bug fix interaction and other stuff |
Systems Genetics v1.0.1
Bug fixes
- Fixed #365 VCF with missing values in samples (./.) cannot be read
