Hoohm CITE-seq-Count issues

Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay

https://hoohm.github.io/CITE-seq-Count/

MIT License

79 stars 44 forks source link

issues

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CITE-seq R1 length issue

#194 Rimanpreet1 opened 2 months ago
11
Convert `columns` from set to list before creating pd.DataFrame()

#193 dtenenba opened 4 months ago
1
ValueError: columns cannot be a set

#192 77babyy opened 6 months ago
3
CITE-seq-Count run gets stuck

#191 Layla-R opened 7 months ago
4
Please, trim all sequences at the same length.

#190 edceeyuchen opened 9 months ago
0
Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?

#189 edceeyuchen closed 9 months ago
2
Does not compile using Python version > 3.9.x please fix.

#188 TheRealQuantumCheese opened 10 months ago
0
Unable to locate temp file while merging results

#187 xmi215 opened 10 months ago
0
add --store-read-ids and --read-ids-whitelist options

#186 lldelisle opened 1 year ago
0
my proposed changes

#185 lldelisle opened 1 year ago
2
Allow to split fastq or get list of readID per cell

#184 lldelisle opened 1 year ago
2
Pandas error after correcting UMIs

#183 ejohnson643 opened 1 year ago
1
Running Cite-Seq-count with next GEM protocol

#181 yeroslaviz opened 1 year ago
2
barcodes with 0s in all protein tags and unmapped roll

#180 Hanxi-002 opened 1 year ago
2
Include path to tag file in run report

#179 johnyaku closed 1 year ago
1
Discussion question -- is it normal to take so long?

#178 dagarfield opened 1 year ago
3
100% unmapped

#177 yls2g13 closed 1 year ago
0
method keeps looking for whitelist when not provided.

#176 naila53 closed 1 year ago
8
bug in preprocessing.py -> get_read_paths() (version 1.4.3)

#175 AlexSurnov closed 1 year ago
1
Cell Hashing on Multiome samples

#174 bassanio opened 1 year ago
11
Python error when there are too many cells? Script never finishes

#173 ejagoda14 opened 2 years ago
2
ValueError: columns cannot be a set

#172 jamesboot opened 2 years ago
5
Code for running multiple lanes

#171 leeanapeters opened 2 years ago
0
Feature/cells argument

#170 Hoohm opened 2 years ago
4
Different "UMIs corrected" results between v1.4.3 and v1.4.5

#169 rosaxma closed 2 years ago
2
Complex whitelist

#168 alanaleah89 opened 2 years ago
2
Percentage unmapped: 100

#167 sopenaml opened 2 years ago
18
CITE-seq-Count for multimodal data

#166 YingzhengXu opened 2 years ago
8
different results each the CITE-seq count is run

#165 colin986 opened 2 years ago
5
Issue with No module named 'Levenshtein'

#164 Lopiniatre closed 2 years ago
2
Max memory limit when running CITE-seq-Count

#163 molybdenumt opened 2 years ago
1
Repeated MemoryError in each ForkPoolWorker

#162 amber4mint opened 3 years ago
0
CITE-seq-Count 100% unmapped

#161 carbycrab opened 3 years ago
9
Proper Saturation Rate Calculation

#160 brindavjk opened 3 years ago
1
Low overlap between cell barcodes and hashtag barcodes

#159 mary77 opened 3 years ago
2
running with totalseqB

#158 naila53 opened 3 years ago
4
Error when option are set to --bc_collapsing_dist 0

#157 rule-110 closed 3 years ago
2
Mapped/Unmapped Reads

#156 jamesboot closed 3 years ago
2
Understanding [expected cells] parameter and [whitelist] parameter

#155 jhjlee opened 3 years ago
2
Running CITE-seq-Count on ASAP-seq

#154 jhjlee closed 3 years ago
7
How can I handle with a separated cell barcode sequence?

#153 suzuki-shm closed 3 years ago
3
barcode bug

#152 craigamartens opened 3 years ago
1
Filtering UMIs on read number

#151 rule-110 closed 2 months ago
1
error running cite-seq-count

#150 fouerghi opened 3 years ago
10
Confusion about input arguments

#149 YingzhengXu closed 3 years ago
4
Excessive memory use in apply_async causing pool to crash

#148 jhasselmann808 opened 3 years ago
5
v1.5.0 resulting in much lower umi counts than v1.4.4 with same settings..?

#147 Erinke89 closed 3 years ago
4
Approximate the cell ranger unfiltered counts output?

#146 bbimber opened 3 years ago
1
Script won't complete

#145 curtisd0886 opened 3 years ago
7
line 592 of processing.py gives UnboundLocalError in 1.5.0

#144 Erinke89 closed 3 years ago
9