Ecosyste.ms: Issues

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GitHub / bioinfo-biols/CIRIquant issues and pull requests

#72 - Some questions about the results of ciriquant

Issue - State: open - Opened by mysolid23 11 days ago

#71 - Add support for single end data and switch to python3

Pull Request - State: open - Opened by nictru about 1 month ago - 2 comments

#69 - install CIRIquant using the recommend way

Issue - State: open - Opened by mysolid23 3 months ago

#68 - Bump scikit-learn from 0.20.3 to 1.5.0

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#67 - invalid syntax in hisat2_read_statistics.py

Issue - State: open - Opened by qj009 4 months ago

#66 - HISAT2 is not working as expected

Issue - State: open - Opened by guillepl 6 months ago

#65 - hisat2-build index for circRNA-seq

Issue - State: open - Opened by fengweimin-maker 6 months ago - 3 comments

#64 - HISAT2 Error: Encountered internal HISAT2 exception (#1）

Issue - State: open - Opened by EdWardYF7 7 months ago - 1 comment

#63 - Hisat2 produces empty bam files

Issue - State: open - Opened by Braulium 8 months ago

#62 - How to get the p-value from DE analysis?

Issue - State: open - Opened by Li-Chengyu 10 months ago

#61 - sample_index does not exist Exiting now

Issue - State: open - Opened by Yonglee1 11 months ago - 3 comments

#60 - Question: Predict circRNAs using multiple tools

Issue - State: closed - Opened by farzamani 11 months ago - 1 comment

#59 - Issue with EdgeR Installation in CIRIquant

Issue - State: closed - Opened by gkibt 11 months ago - 11 comments

#58 - KeyError

Issue - State: closed - Opened by stefanerb89 about 1 year ago

#57 - CIRIquant for stranded paired-end reads(dUTP method)

Issue - State: open - Opened by junjunlab about 1 year ago - 1 comment

#56 - Bump scipy from 1.2.2 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#55 - Error in prepDE.py

Issue - State: closed - Opened by chickenHyop over 1 year ago - 4 comments

#54 - Alignment does not end

Issue - State: closed - Opened by kendaida over 1 year ago

#53 - full-length sequence of circRNA

Issue - State: open - Opened by Zheng19w over 1 year ago - 3 comments

#52 - multiple fastq files

Issue - State: open - Opened by sung over 1 year ago - 1 comment

#51 - Limitation on Number of Samples Used/DE Filtering Issue?

Issue - State: open - Opened by mlvanhorn over 1 year ago - 1 comment

#50 - Error while running CIRIquant

Issue - State: open - Opened by nandakumaryellapu over 1 year ago - 7 comments

#47 - Problem with installation of CIRIquant

Issue - State: closed - Opened by choijamtsmunkhzul over 1 year ago

#46 - Small gtf file issue

Issue - State: open - Opened by Boltzz98 over 1 year ago

#45 - Deferentially expressed circRNAs with biological replicate

Issue - State: closed - Opened by ravisaroch almost 2 years ago - 1 comment

#44 - `os.chmod` error in containers

Pull Request - State: closed - Opened by BarryDigby almost 2 years ago - 4 comments

#43 - How to measure whether circRNAs are significantly different

Issue - State: open - Opened by litao1503 about 2 years ago

#40 - Error in 'Detecting FSJ reads from genome alignment file'

Issue - State: open - Opened by stefanerb89 about 2 years ago - 2 comments

#39 - Bump numpy from 1.16.4 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#38 - .log show successful completion, but there is no file

Issue - State: open - Opened by algaebrown over 2 years ago - 3 comments

#36 - change the permissions on 'CIRI2.pl' while running CIRIquant on cluster

Issue - State: open - Opened by MaryamLabaf over 2 years ago - 3 comments

#35 - .fa is empty, index does not exist

Issue - State: open - Opened by algaebrown over 2 years ago - 4 comments

#34 - Very low numbers for circular RNAs

Issue - State: open - Opened by FerallOut over 2 years ago - 3 comments

#33 - About CircAtlas sequence length

Issue - State: open - Opened by andre-gabriel-42 over 2 years ago - 4 comments

#32 - Issue running prepDE.py

Issue - State: open - Opened by G-Molano-LA over 3 years ago - 3 comments

#31 - Encountered internal HISAT2 exception (#1)

Issue - State: closed - Opened by cjs0617 over 3 years ago - 8 comments

#30 - Issue with using find_circ prediction results for CIRIquant

Issue - State: open - Opened by prisca399 over 3 years ago - 1 comment

#29 - Generate empty gtf file

Issue - State: closed - Opened by mrb20045 over 3 years ago - 10 comments

#28 - About BSJs and FSJs

Issue - State: closed - Opened by andre-gabriel-42 over 3 years ago - 2 comments

#27 - Bump pyyaml from 5.1.1 to 5.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#26 - EdgeR in CIRI_DE_replicate issue

Issue - State: closed - Opened by andre-gabriel-42 over 3 years ago - 7 comments

#25 - duplicate rows R error in CIRI_DE_replicate

Issue - State: closed - Opened by eltonjrv over 3 years ago - 5 comments

#24 - Not able to generate the final circ.gtf output

Issue - State: closed - Opened by eltonjrv over 3 years ago - 4 comments

#23 - Rowname error with CIRI_DE_replicate command

Issue - State: closed - Opened by prisca399 over 3 years ago - 2 comments

#22 - Different circRNA prediction tools for differential expression

Issue - State: closed - Opened by prisca399 over 3 years ago - 4 comments

#21 - Read count cut-off for circRNA differential expression

Issue - State: closed - Opened by prisca399 over 3 years ago - 6 comments

#20 - Add check.names=FALSE in CIRI_DE.R

Pull Request - State: closed - Opened by osagiei over 3 years ago - 1 comment

#19 - Can CIRIquant be used with single-end data?

Issue - State: closed - Opened by stiv1n over 3 years ago - 3 comments

#18 - why miss so many circRNA to putout ?

Issue - State: closed - Opened by gnilihzeux almost 4 years ago - 8 comments

#17 - KeyError: 'chr1_89476615_89476806'

Issue - State: closed - Opened by gnilihzeux almost 4 years ago - 3 comments

#16 - Question regarding RNaseR corretion

Issue - State: closed - Opened by baylorbiostat almost 4 years ago - 1 comment

#15 - index not built

Issue - State: closed - Opened by stfacc about 4 years ago - 4 comments

#14 - --RNaseR: command not found

Issue - State: closed - Opened by hernerrrrr about 4 years ago - 1 comment

#13 - Options for single-end data entry

Issue - State: closed - Opened by NextExon over 4 years ago - 1 comment

#12 - DE with Biological Replicates Step 3 Error

Issue - State: closed - Opened by mlvanhorn over 4 years ago - 11 comments

#11 - Large DS Scores for Unexpressed Genes

Issue - State: closed - Opened by DarioS over 4 years ago - 1 comment

#10 - Biologist Suggestion: Text Summary Tables

Issue - State: closed - Opened by DarioS over 4 years ago - 2 comments

#9 - CIRI2 Missing FIle Error

Issue - State: closed - Opened by DarioS over 4 years ago - 5 comments

#8 - Automatically Delete Intermediate Files

Issue - State: closed - Opened by DarioS over 4 years ago
Labels: enhancement

#7 - More Precise Definition of Options

Issue - State: closed - Opened by DarioS over 4 years ago - 3 comments

#6 - Cannot serialize a string larger than 2 GB

Issue - State: closed - Opened by solo7773 over 4 years ago - 1 comment

#5 - chr1.fa.bwt, not found

Issue - State: closed - Opened by solo7773 over 4 years ago - 1 comment

#4 - quantification and differential expression analysis for RNase R treated samples

Issue - State: closed - Opened by cuijr1995 over 4 years ago - 2 comments

#3 - Add support for strand specific RNA-seq data

Issue - State: closed - Opened by Kevinzjy almost 5 years ago - 6 comments
Labels: enhancement

#2 - Error in circ_type when using annotation from UCSC table browser

Issue - State: closed - Opened by Kevinzjy almost 5 years ago - 1 comment
Labels: bug

#1 - Installation error

Issue - State: closed - Opened by ysbioinfo over 5 years ago - 3 comments