COMBINE-lab alevin-fry issues

COMBINE-lab / alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

https://alevin-fry.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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issues

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Concatenate multiple map.rad files generated by pisecem/salmon and run alevin-fry generate-permit-list, collate and quant

#143 nihanasam8 closed 3 weeks ago
22
merge master back into develop

#142 rob-p closed 3 months ago
0
add cargo dist workflow

#141 rob-p closed 3 months ago
0
chore(master): release 0.9.0

#140 github-actions[bot] closed 3 months ago
0
Develop

#139 rob-p closed 3 months ago
0
ExitStatus(unix_wait_status(6))

#138 Anto9393 closed 3 months ago
24
How to realize umi-tools directional algorithm in alevin-fry

#137 tengdiyouying608 closed 3 months ago
5
only 100 cells output from feature barcoding data

#136 crazyhottommy closed 4 months ago
19
merge master back into dev

#135 rob-p closed 4 months ago
0
CorrectedReads in featureDump.txt

#134 wangjiawen2013 opened 4 months ago
0
almost no genes detected

#133 wangjiawen2013 opened 5 months ago
0
zero-length barcode

#132 wangjiawen2013 opened 5 months ago
2
The barcode or umi spans multi reads

#131 wangjiawen2013 closed 5 months ago
7
Don't correct barcodes

#130 wangjiawen2013 closed 5 months ago
1
Cannot get output

#129 wangjiawen2013 closed 5 months ago
2
Using genotype based demultiplexing tools on alevin-fry output

#128 changostraw opened 5 months ago
1
Merging replicates with different permit lists

#127 ardecasien opened 7 months ago
2
Request for a decoy-aware index in alevin-fry (with a specific case)

#126 dburguera closed 7 months ago
6
request for a tutorial using alevin-fry for multiome datasets

#125 klai001 opened 8 months ago
0
Alevin-fry for SMARt-seq3 data

#124 ssuthram-gilead opened 8 months ago
0
Fix first two links in docs overview

#123 jaclyn-taroni closed 8 months ago
1
technical limitation to bc length?

#122 sisterdot closed 7 months ago
2
alevin-fry not generating all required output files

#121 AnnaAMonaco closed 8 months ago
6
Feature request: Support for 10x "flex" fixed RNA data

#120 pakiessling opened 9 months ago
3
Update documentation to include recommended processing for 10x scRNA 5' V2

#118 jeremymsimon opened 11 months ago
2
chore(master): release 0.8.2

#116 github-actions[bot] closed 1 year ago
1
Develop

#115 rob-p closed 1 year ago
0
Unmaintained dependency used by alevin fry

#114 kbipinkumar closed 1 year ago
1
Raw and filtered count data similar to cell ranger output.

#113 bk11-lab opened 1 year ago
0
File formats for --dump-eqclasses

#112 davidaknowles closed 1 year ago
4
Only getting DIR:false after collate of SPLIT-seq

#111 davidaknowles closed 1 year ago
2
typo correction

#110 liujamin closed 1 year ago
1
Difference in expression when used salmon-alevin vs alevin-fry

#109 sdr08 closed 1 year ago
11
Multimapping issue

#108 lcmmichielsen closed 1 year ago
5
What is the difference between generate-permit-list --expected-ori "either" and "both"?

#107 ColeWunderlich closed 1 year ago
2
Feature request - Rhapsody whole genome sequences

#106 stela2502 opened 1 year ago
9
Update README.md

#105 rob-p closed 1 year ago
0
Merge master back into develop

#104 rob-p closed 1 year ago
0
Documentation "quick-start"

#103 schmucr1 opened 1 year ago
11
How to make alevin-fry --expect cells to be better at guessing the number of cells?

#102 ljudevitluka opened 1 year ago
3
Update Cargo.toml

#100 rob-p closed 1 year ago
0
Merge pull request #97 from COMBINE-lab/master

#99 rob-p closed 1 year ago
0
chore(master): release 0.8.1

#98 github-actions[bot] closed 1 year ago
1
Update rust.yml

#97 rob-p closed 1 year ago
0
Clap v4

#96 rob-p closed 1 year ago
0
quant not exiting with correct error code

#95 ATpoint closed 1 year ago
2
doc on read geometry

#94 fransua closed 1 year ago
1
fix typo

#93 Gaura closed 1 year ago
0
Merge master changes back into develop

#92 rob-p closed 1 year ago
0
Calculating spliced/unpliced ratio and what to do with the ambigous count

#90 mdmanurung closed 1 year ago
2