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LuyiTian
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scPipe
a pipeline for single cell RNA-seq data analysis
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Update README.md
#156
shaniAmare
closed
11 months ago
1
Update scPipe_atac_tutorial.Rmd
#155
shaniAmare
closed
11 months ago
0
Fixed bug in `sc_atac_create_fragments` where no output file was being produced.
#154
OliverVoogd
closed
1 year ago
0
ATAC Vignette Build error fix for windows
#153
OliverVoogd
closed
1 year ago
0
Windows ATAC vignette fixed
#152
OliverVoogd
closed
1 year ago
0
Synchronised to Bioconductor
#151
Shians
closed
1 year ago
0
Bioc Checks passed with some warnings remaining
#150
shaniAmare
closed
1 year ago
1
Fully functional scATAC-Seq preprocessing module
#149
shaniAmare
closed
2 years ago
0
PR for the version as of 9/9/22 : multiome integration ongoing
#148
shaniAmare
closed
2 years ago
0
Fixes #146
#147
Shians
closed
2 years ago
0
Bug in report_template.Rmd
#146
PeteHaitch
closed
2 years ago
1
Addressed some BiocCheck complaints and spelling errors
#145
Shians
closed
2 years ago
0
scATAC-Seq preprocessing functionality update
#144
shaniAmare
closed
2 years ago
0
Error in sc_trim_barcode
#143
satzel
closed
2 years ago
7
Release 3 14
#142
LuyiTian
closed
2 years ago
0
Port #140 from devel branch to fix #136 in release branch
#141
PeteHaitch
closed
2 years ago
1
Update report_template.Rmd
#140
OliverVoogd
closed
2 years ago
1
Update biomart_methods.R
#139
OliverVoogd
closed
2 years ago
1
sc_trim_barcode problem in single-end data
#138
MiladAD123NGS
opened
2 years ago
1
Read structure for CELseq protocol swaps R1 and R2
#137
mcmero
opened
3 years ago
0
scater::calculateQCMetrics is deprepated
#136
bernt-matthias
opened
3 years ago
0
automatically load biomaRt?
#135
bernt-matthias
opened
3 years ago
0
sc-exon-mapping strand checking
#134
parsboy66
opened
3 years ago
2
UMI counts with N bases
#133
ljgearing
closed
3 years ago
2
Use `drop = FALSE` when subsetting matrices
#132
PeteHaitch
closed
3 years ago
0
sc_demultiplex empty output
#131
cpattaroni
opened
3 years ago
1
Fixing build
#130
Shians
closed
3 years ago
0
[E::bam_aux_get] Corrupted aux data
#129
cpattaroni
closed
3 years ago
1
Data processing for Smart-seq2 data
#128
arshiyaakeel
opened
4 years ago
0
Changed hashmap to hash because hashmap is deprecated
#127
Shians
closed
4 years ago
0
Fixed bug with setting organism and gene_id_type in create_processed_report()
#126
Shians
closed
4 years ago
0
Fixes #124
#125
Shians
closed
4 years ago
0
Error in FUN(...) while doing “create_processed_report”
#124
zoe106
closed
4 years ago
8
transcript ID not found
#123
AmaliT
opened
5 years ago
1
All data (including example data) producing gene count matrix with 0s
#122
IzzyJRussell
opened
5 years ago
5
gff3 gene ID replaced by random numbers in gene_count.csv table
#121
audreystott
opened
5 years ago
1
Fixed '~' not being expanded for output files and folders
#120
Shians
closed
5 years ago
0
Fixes #117
#119
Shians
closed
5 years ago
4
sc_gene_counting(..., UMI_cor = 0) is documented but gives error
#118
PeteHaitch
closed
5 years ago
1
Column length error
#117
audreystott
closed
5 years ago
2
Error in readGFF
#116
audreystott
closed
5 years ago
2
Running multiple instances of scPipe
#115
bhavnah
closed
5 years ago
8
Processing samples from multiple individuals for joint analysis
#114
bioinfnewb
closed
5 years ago
5
"UMI_duplication_count.csv" file and "UMI_dedup_stat.csv" file
#113
shokohirosue
closed
5 years ago
5
number of cells and genes
#112
shokohirosue
closed
5 years ago
10
Setting up a usage gallery
#111
LTLA
opened
5 years ago
2
No such file or directory error in `create_sce_by_dir`
#110
zhewa
closed
5 years ago
1
Modified code to remove check warnings
#109
Shians
closed
5 years ago
0
Fixed sc_trim_fastq() not working when outfq is just a file name with no parent folder
#108
Shians
closed
5 years ago
2
check bam tag in function
#107
LuyiTian
opened
5 years ago
0
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