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[Bug]: The processByBam now is always TRUE in single cell mode

Status: Open.

#571 In GoekeLab/bambu;

· SuiYue-2308 opened on Apr 17, 2026

add functionality to write to GFF file

code architecturerefers to code modularisation & data flow [presets, argument, input/output data type] in bamburefers to code modularisation & data flow [presets, argument, input/output data type] in bambu

Status: Open.

Feature

#564 In GoekeLab/bambu;

· hafiz-ismail opened on Apr 16, 2026

summarise by exon count

othersimprovements that do not belong to any of the other categoriesimprovements that do not belong to any of the other categories

Status: Open.

Feature

#563 In GoekeLab/bambu;

· ch99l opened on Apr 16, 2026

BiocParallel error

Status: Open.

#551 In GoekeLab/bambu;

· sophiachen1 opened on Apr 4, 2026

Error in sparse.model.matrix when only one unique transcript is in the matrix

Status: Open.

#549 In GoekeLab/bambu;

· lingminhao opened on Mar 23, 2026

Large-scale data selection: select multiple samples (bulk data) for comparing the results from different branches.

Status: Open.

#544 In GoekeLab/bambu;

· SuiYue-2308 opened on Mar 6, 2026

BiocParallel errors when running bambu

Status: Open.

#541 In GoekeLab/bambu;

· lyj95618 opened on Feb 12, 2026

which version of xgboost is ok?

Status: Open.

#539 In GoekeLab/bambu;

· lingfengxu opened on Feb 9, 2026

High NDR values when quantifying transposable elements in exosomes

Status: Open.

#536 In GoekeLab/bambu;

· NaixiangYu opened on Jan 29, 2026

error when using bambu to quantify SIRV

Status: Open.

#532 In GoekeLab/bambu;

· yinshiyi opened on Jan 20, 2026

unittest to be updated for devel_pre_v4

Status: Open.

#530 In GoekeLab/bambu;

· cying111 opened on Jan 15, 2026

Dependency issues when installing

Status: Open.

#523 In GoekeLab/bambu;

· sophiachen1 opened on Jan 11, 2026