NEWS.md

In HAN-Siyu/ncProR: Predicting Long non-coding RNA-Protein Interaction

LION 0.3.0.0

• Support assigning additional arguments for RNAsubopt and Predator.

LION 0.2.9.1

• Fix the remaining issue in metric calculation (see explanation in v0.2.9) during the retraining of LION. Thanks to @Ci-TJ (Qin Lin) for pointing this out.

LION 0.2.9

• Fix bug in evaluatePrediction(): This bug makes the function always take the first level as positive label, yielding wrong values for some metrics (such as sensitivity, specificity, etc) when the first level is negative. This issue made no effect on the results reported in LION's paper.

LION 0.2.8

• mtry can be tuned.

LION 0.2.7

• Update models.

LION 0.2.6

• Update reference manual.
• Bugs fixed.

LION 0.2.5

• Update reference manual.
• Bugs fixed.

LION 0.2.4

• Users can use run_confidentPrediction() to get prediction results of multiple methods in one run.
• Update reference manual.
• Bugs fixed.

LION 0.2.3

• Add run_LncADeep() for prediction using LncADeep's feature set.
• Add computeMLC() to compute the most-like CDS (MLC) region.
• Add parameter EDP which supports applying entropy density profile to sequence intrinsic features.
• Update reference manual.
• Bugs fixed.

LION 0.2.2

• Matthews correlation coefficient (MCC) is included into evaluation metrics.
• TP, TN, FP and FN are reported in evaluation results.
• Add evaluatePrediction() for prediction evaluation.
• Bugs fixed.

LION 0.2.1

• Add argument verification.
• Update reference manual.
• Bugs fixed.

LION 0.2.0

• "retrain" and "feature" modes are added to function run_LION(), run_RPISeq(), run_lncPro() and run_rpiCOOL(). Now users can use ready-to-use functions to extract features or retrain the models of LION, RPISeq, lncPro and rpiCOOL.
• External parallel cores can be passed to functions.
• Internal changes to improve efficiency.
• Update reference manual.
• Bugs fixed.

LION 0.1.0

• Original release

HAN-Siyu/ncProR documentation built on Nov. 3, 2023, 12:08 a.m.