Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / mhalushka/miRge3.0 issues and pull requests

#100 - 'bins' Error while running miRge3.0

Issue - State: open - Opened by ChenSchiff 3 months ago - 4 comments

#99 - Python bug

Issue - State: open - Opened by Cristinex 3 months ago - 1 comment

#98 - Bump scikit-learn from 0.23.1 to 1.5.0

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

#97 - Issue running mirge3

Issue - State: open - Opened by hopekro 5 months ago - 1 comment

#96 - Trimming repeated nucleotides

Issue - State: open - Opened by adamcatto 5 months ago - 2 comments

#95 - Unmapped reads

Issue - State: open - Opened by hamzaaitabbou96 5 months ago - 1 comment

#94 - Samples with different adapters

Issue - State: open - Opened by adamcatto 5 months ago - 3 comments

#93 - Issues with counts and adapters

Issue - State: open - Opened by VilainLab 6 months ago - 1 comment

#91 - Does miRge3.0 restrict reverse-complement mapping?

Issue - State: closed - Opened by MilosCRF 9 months ago - 2 comments

#90 - mirge3 killde

Issue - State: open - Opened by voluptatis 9 months ago - 5 comments

#88 - Error while running miRge3.0

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

#87 - Question about Read Length Distribution

Issue - State: closed - Opened by hy101 11 months ago - 3 comments

#86 - UMI

Issue - State: open - Opened by hamzaaitabbou96 11 months ago - 1 comment

#85 - installation on mac OS

Issue - State: open - Opened by rolfsoekilde 12 months ago - 16 comments

#84 - Spike-In

Issue - State: open - Opened by hamzaaitabbou96 about 1 year ago - 1 comment

#83 - db versions

Issue - State: closed - Opened by knokknok about 1 year ago - 7 comments

#82 - differentially expressed hairpin miRNA

Issue - State: closed - Opened by mick42-star about 1 year ago - 1 comment

#81 - installation with mac os

Issue - State: closed - Opened by mick42-star about 1 year ago - 2 comments

#80 - Cannot set a DataFrame with multiple columns to the single column miRNA_cbind

Issue - State: closed - Opened by imranjesar about 1 year ago - 3 comments

#79 - Revert "Ambiguous alignment handling"

Pull Request - State: closed - Opened by arunhpatil about 1 year ago

#78 - Error when running miRge3.0: ValueError in summarize function

Issue - State: closed - Opened by shashankpritam about 1 year ago - 6 comments

#77 - Output bam not complete

Issue - State: open - Opened by Glfrey about 1 year ago - 15 comments

#76 - miRge3.0 not accepting the path to mirge libraries

Issue - State: closed - Opened by imranjesar about 1 year ago - 6 comments

#75 - miRbase Annotation Discrepancies

Issue - State: closed - Opened by asucrer over 1 year ago - 2 comments

#74 - Ambiguous alignment handling

Pull Request - State: closed - Opened by Glfrey over 1 year ago - 18 comments

#73 - Numpy versioning issues

Issue - State: closed - Opened by Glfrey over 1 year ago - 1 comment

#72 - Question about SNPs and Library

Issue - State: open - Opened by John-Drake over 1 year ago - 9 comments

#71 - Alignment behaviour query

Issue - State: closed - Opened by Glfrey over 1 year ago - 8 comments

#70 - Added exact miRNA output

Pull Request - State: closed - Opened by Glfrey over 1 year ago - 2 comments

#69 - Added ability to extract counts for exact miRNAs

Pull Request - State: closed - Opened by Glfrey over 1 year ago - 1 comment

#68 - Custom identifiers for tRFs

Issue - State: closed - Opened by RoseString over 1 year ago - 2 comments

#67 - Annotation database access

Issue - State: closed - Opened by Glfrey over 1 year ago - 2 comments

#66 - Add '.fq' and '.fq.gz' to accepted file extensions

Issue - State: closed - Opened by mckellardw over 1 year ago - 3 comments

#65 - miRNA reference database

Issue - State: closed - Opened by hamzaaitabbou96 over 1 year ago - 1 comment

#64 - Conda wrong Bowtie version

Issue - State: closed - Opened by Glfrey over 1 year ago - 2 comments

#63 - AttributeError: module 'numpy' has no attribute 'bool'.

Issue - State: closed - Opened by Glfrey over 1 year ago - 3 comments

#62 - miRNA filtration question

Issue - State: closed - Opened by Glfrey over 1 year ago - 2 comments

#61 - Novel miRNA annotation hanging?

Issue - State: closed - Opened by Glfrey over 1 year ago - 24 comments

#60 - Resume error

Issue - State: closed - Opened by Glfrey over 1 year ago - 3 comments

#59 - Update doc for a link o a docker file

Issue - State: closed - Opened by bchatelet almost 2 years ago - 2 comments

#58 - Wrong versions packages in the install doc

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

#57 - visualization.HTML output is empty

Issue - State: closed - Opened by TomRivas almost 2 years ago - 6 comments

#56 - SNP fasta file (human_mirna_SNP_pseudo_miRBase.fa)

Issue - State: open - Opened by taeyoungh about 2 years ago - 11 comments

#55 - Bowtie error

Issue - State: closed - Opened by sanatbhadsavle about 2 years ago - 5 comments

#54 - Log2FC Values Question?

Issue - State: closed - Opened by Samir-A about 2 years ago - 2 comments

#53 - Bam flag question

Issue - State: closed - Opened by bbeniah about 2 years ago - 1 comment

#52 - Annotation for miRNAs

Issue - State: closed - Opened by John-Drake about 2 years ago - 1 comment

#51 - Error with Alignment when performing differential expression analysis

Issue - State: closed - Opened by Samir-A about 2 years ago - 24 comments

#50 - Question about parameters

Issue - State: closed - Opened by Ben7124 about 2 years ago - 1 comment

#49 - Process hanging/killed at collapsing step

Issue - State: closed - Opened by Ben7124 about 2 years ago - 2 comments

#48 - Spike-In

Issue - State: closed - Opened by hamzaaitabbou96 over 2 years ago - 2 comments

#47 - TypeError in Summarizing and tabulating results on macOS

Issue - State: closed - Opened by jofa123 over 2 years ago - 2 comments

#46 - UMI processing

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

#45 - Parser.py missing AdapterParser in cutadapt

Issue - State: closed - Opened by lucascpantaleao over 2 years ago - 15 comments

#44 - I can't get the same total counts using the GFF.

Issue - State: closed - Opened by saneglaz over 2 years ago

#43 - cutadapt not found!. Required: cutadapt >=2.6

Issue - State: closed - Opened by cf-Rachel over 2 years ago - 1 comment

#42 - Is my code working

Issue - State: closed - Opened by tetty988 over 2 years ago - 1 comment

#41 - how to use -dex DESeq2 analysis

Issue - State: closed - Opened by SamWell16 over 2 years ago - 1 comment

#40 - code to train SVM from miRge2.0 paper

Issue - State: closed - Opened by juancarlosfdc over 2 years ago - 7 comments

#39 - miRge3_visualization.html empty

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

#38 - Novel miRNAs error

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

#37 - RNAfold error

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

#36 - Start analysis from collapsed reads

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

#35 - Strand assignment in bam output files

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

#34 - maximum sample number to run and etc.

Issue - State: closed - Opened by juyeong-yi over 2 years ago - 9 comments

#33 - Error while trying to do differential expression

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

#32 - error

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

#31 - Bowtie not found (After Conda installation)

Issue - State: closed - Opened by asucrer over 2 years ago - 9 comments

#30 - Different "miRge3.0 --help"

Issue - State: closed - Opened by schmucr1 almost 3 years ago - 6 comments

#29 - Which file to use for deseq to analyse tRF differential expression?

Issue - State: closed - Opened by seulalee1008 almost 3 years ago - 5 comments

#28 - UMI output files

Issue - State: closed - Opened by francois-a almost 3 years ago - 1 comment

#27 - using spike-in funcitonality

Issue - State: closed - Opened by zuta-osa77 almost 3 years ago - 3 comments

#26 - Predicting novel miRNAs error

Issue - State: closed - Opened by seulalee1008 almost 3 years ago - 4 comments

#24 - Installation conflict

Issue - State: closed - Opened by xielab2017 almost 3 years ago - 12 comments

#23 - question regarding crThreshold

Issue - State: closed - Opened by fmughal almost 3 years ago - 2 comments

#22 - Mapped.csv miR does not equel to miR.Counts.csv

Issue - State: closed - Opened by ray1919 almost 3 years ago - 2 comments

#21 - Cutadapt error for GUI on mac

Issue - State: closed - Opened by senukobla almost 3 years ago - 13 comments

#20 - adaptor trimming

Issue - State: closed - Opened by Cristinex almost 3 years ago - 9 comments

#19 - subprocess.CalledProcessError on docker miRge3.0

Issue - State: closed - Opened by Kotake1993 about 3 years ago

#18 - The following module(s) are unknown: "bowtie"

Issue - State: closed - Opened by ramostapiai about 3 years ago - 13 comments

#17 - Questions

Issue - State: closed - Opened by sagarutturkar about 3 years ago - 2 comments

#16 - Problem with bam file output

Issue - State: closed - Opened by smackenz1 about 3 years ago - 7 comments

#15 - Merge pull request #14 from mhalushka/master

Pull Request - State: closed - Opened by arunhpatil over 3 years ago

#14 - Updated the master

Pull Request - State: closed - Opened by arunhpatil over 3 years ago

#13 - Bowtie error

Issue - State: closed - Opened by NgianZhenKai over 3 years ago - 15 comments

#12 - Installing miRge3.0 on Windows - Error: "Failed building wheel for isal"

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

#11 - ValueError: `bins` must be positive, when an integer

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

#10 - quick question and reading into memory

Issue - State: closed - Opened by waleadebayo over 3 years ago - 1 comment

#9 - error

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

#8 - bowtie -x index option failure

Issue - State: closed - Opened by FrAoJm almost 4 years ago - 6 comments

#7 - How to input paired-end sequencing data？

Issue - State: closed - Opened by wan230114 almost 4 years ago - 2 comments

#6 - Sample data running error.

Issue - State: closed - Opened by wan230114 almost 4 years ago - 1 comment

#5 - Create LICENSE

Pull Request - State: closed - Opened by arunhpatil almost 4 years ago

#4 - Bump pyxdg from 0.25 to 0.26

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#3 - Bump urllib3 from 1.22 to 1.24.2

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#2 - Bump httplib2 from 0.9.2 to 0.18.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#1 - Bump pyyaml from 3.12 to 5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies