Ecosyste.ms: Issues

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

GitHub / tomazc/iCount issues and pull requests

#215 - Could iCount xlsites support soft-clipping?

Issue - State: open - Opened by TomSmithCGAT 9 months ago

#212 - Help with installation

Issue - State: open - Opened by valerieT1998 over 1 year ago - 1 comment

#211 - permutation test for multi-mapped reads

Issue - State: closed - Opened by HibaLaghrissi almost 2 years ago

#210 - How to cite update

Issue - State: open - Opened by michaelmhoffman over 2 years ago

#208 - Adding multithreading option for cutadapt and demultiplex sub commands

Pull Request - State: open - Opened by skchronicles almost 3 years ago - 3 comments

#207 - iCount demultiplex --minimum_length cannot work

Issue - State: open - Opened by wjzhangiris about 3 years ago

#206 - issue with indexstar

Issue - State: open - Opened by vd77 about 3 years ago

#205 - Application of iCount in Arabidopsis (plants) causes errors.

Issue - State: closed - Opened by Linhua-Sun about 4 years ago - 2 comments

#204 - Snakemake

Pull Request - State: open - Opened by Faitero about 4 years ago - 2 comments

#203 - Error in demultiplex.py with 3' barcode

Pull Request - State: open - Opened by CharlotteAnne about 4 years ago - 1 comment
Labels: bug

#202 - Clusters command generates empty file

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

#201 - iCount clusters: error

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

#200 - Error in generating segments

Issue - State: closed - Opened by garimak05 over 4 years ago - 2 comments

#199 - Setup fails with pip install

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

#198 - merge feat test data with master

Pull Request - State: closed - Opened by CharlotteAnne over 4 years ago - 1 comment
Labels: enhancement

#197 - Snakemake

Pull Request - State: closed - Opened by Faitero over 4 years ago

#196 - Snakemake

Pull Request - State: closed - Opened by Faitero almost 5 years ago - 1 comment

#195 - Snakemake

Pull Request - State: closed - Opened by Faitero almost 5 years ago - 2 comments

#194 - star: Fix shared memory use, resolves #169

Pull Request - State: closed - Opened by tomazc about 5 years ago - 1 comment

#193 - license: Update license and copyright

Pull Request - State: closed - Opened by tomazc about 5 years ago

#192 - env: Add support for python 3.7

Pull Request - State: closed - Opened by tomazc over 5 years ago - 1 comment

#191 - Question: iCount xlsites expected runtime

Issue - State: open - Opened by mirax87 over 5 years ago - 2 comments

#190 - setup.py: Add missing comma

Pull Request - State: closed - Opened by JureZmrzlikar over 5 years ago - 1 comment

#189 - Enable 3' barcode demultiplex

Pull Request - State: closed - Opened by JureZmrzlikar over 5 years ago - 2 comments

#188 - Rework RNA-maps

Pull Request - State: closed - Opened by JureZmrzlikar almost 6 years ago - 8 comments

#187 - setup: Fix docker build and BED formatting issues in bedtools, fixes #174

Pull Request - State: closed - Opened by tomazc about 6 years ago - 1 comment

#186 - segment:error in gene level segmentation

Issue - State: open - Opened by snk9987 over 6 years ago - 1 comment

#185 - xlsites: Add max_barcodes parameter

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 1 comment

#184 - bedgraph: support additional track-configuring parameters

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 1 comment

#183 - SyntaxError Invalid syntax

Issue - State: closed - Opened by krutru over 6 years ago - 2 comments

#182 - tests: small fixes, problem accessing FTP in Travis

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 1 comment

#181 - Small fixes in xlsites module

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 3 comments

#180 - [E::bgzf_flush] File write failed (wrong size)

Issue - State: closed - Opened by sarahbonnin over 6 years ago - 2 comments

#179 - confusion between --mapq_th and --multimax in iCount xlsites

Issue - State: closed - Opened by YannAudic over 6 years ago - 2 comments

#178 - demultiplex: Handle case of empty demultiplexed file

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 1 comment

#177 - segment: Correct the name of regions file

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago

#176 - trouble understanding the cDNA % in the summary gene report

Issue - State: closed - Opened by YannAudic over 6 years ago - 4 comments

#175 - linters: Set line length to 119

Pull Request - State: closed - Opened by JureZmrzlikar over 6 years ago - 1 comment

#174 - iCount clusters fails to predict clusters with bedtools 2.27 - no error or warning

Issue - State: closed - Opened by mirax87 almost 7 years ago - 3 comments

#173 - summary: Refactor reports

Pull Request - State: closed - Opened by JureZmrzlikar almost 7 years ago - 3 comments

#172 - gencode: Download primary assembly of genome/annotation

Pull Request - State: closed - Opened by JureZmrzlikar almost 7 years ago - 3 comments

#171 - demultiplex: Support barcodes with different sizes

Pull Request - State: closed - Opened by JureZmrzlikar almost 7 years ago - 1 comment

#170 - add --genomeLoad LoadAndRemove

Pull Request - State: closed - Opened by bakerwm almost 7 years ago - 2 comments

#169 - Suggest: '--genomeLoad', 'LoadAndRemove' for STAR

Issue - State: closed - Opened by bakerwm almost 7 years ago - 3 comments

#168 - bedgraph: Add BED to bedGraph converter

Pull Request - State: closed - Opened by JureZmrzlikar almost 7 years ago - 3 comments

#167 - Fix type of ``ratio_th`` to float

Pull Request - State: closed - Opened by JureZmrzlikar about 7 years ago - 1 comment

#166 - xlsites: Fix randomer counting

Pull Request - State: closed - Opened by tomazc about 7 years ago - 2 comments

#165 - star: Add optional arguments to control memory usage, related to #134

Pull Request - State: closed - Opened by tomazc about 7 years ago - 1 comment

#164 - Error while running iCount peaks

Issue - State: closed - Opened by raflynn about 7 years ago - 6 comments

#163 - genomes: Make release of type str

Pull Request - State: closed - Opened by JureZmrzlikar about 7 years ago - 1 comment

#162 - tests: Set random seed

Pull Request - State: closed - Opened by JureZmrzlikar about 7 years ago - 1 comment

#161 - genomes: Add GENCODE as source of genome and annotation

Pull Request - State: closed - Opened by JureZmrzlikar about 7 years ago - 5 comments

#160 - xlsites: Minor fix in processing bam file

Pull Request - State: closed - Opened by JureZmrzlikar about 7 years ago - 1 comment

#159 - tests: e2e tests framework and rnamaps example

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#158 - Definitions from 'summary' tool

Issue - State: open - Opened by raflynn over 7 years ago - 1 comment

#157 - Memory Issue - Running 'peaks' tool

Issue - State: open - Opened by raflynn over 7 years ago

#156 - clusters: Cluster peaks then quantify using sites

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#155 - installation

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

#154 - release: Register and upload package on PyPI

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#153 - docs: Fix MANIFEST.in to exclude presentations

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#152 - docs: Add Crick presentation, minor changes to tutorial

Pull Request - State: closed - Opened by tomazc over 7 years ago

#151 - clusters: Fix saving of gziped files

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#150 - annotate: Fix tests

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#149 - docs: minor changes to tutorial

Pull Request - State: closed - Opened by tomazc over 7 years ago

#148 - docs: Improve tutorial example, add matplotlib

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#147 - xlsites: improve memory efficiency

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#146 - metrics: Make all analysis return metrics objects

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#145 - fastq: additional refactoring

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 2 comments

#144 - doc: Add docs on docker, virtualbox, contrib, lzma and bz2 dev libs

Pull Request - State: closed - Opened by tomazc over 7 years ago - 1 comment

#143 - cli: Fix output of iCount --version in case of missing folders, closes #142

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 2 comments

#142 - iCount --version polluted by TMP_ROOT creation message

Issue - State: closed - Opened by JureZmrzlikar over 7 years ago

#141 - demultiplex: refactor and fix random barcode appending

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 5 comments

#139 - Support Prokaryotic Genomes

Issue - State: open - Opened by Faitero over 7 years ago - 5 comments

#138 - ensembl: Support versions up to 88.

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#137 - Small fixes

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 2 comments

#136 - xlsites: Fix generation of 'skipped file'

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 1 comment

#135 - rnamaps: Add normalization, closes #21

Pull Request - State: closed - Opened by JureZmrzlikar over 7 years ago - 4 comments

#134 - Support custom arguments in mapstar and indexstar

Issue - State: open - Opened by JureZmrzlikar almost 8 years ago
Labels: enhancement

#133 - cli: Improve descriptions, resolves #131

Pull Request - State: closed - Opened by JureZmrzlikar almost 8 years ago - 3 comments

#132 - segment: Support GENCODE annotations, resolves #125

Pull Request - State: closed - Opened by JureZmrzlikar almost 8 years ago - 1 comment

#131 - iCount mapstar do not accept "--runThreadN" comand

Issue - State: closed - Opened by Faitero almost 8 years ago - 2 comments

#130 - Problems connecting to ENSEMBL FTP server

Issue - State: open - Opened by Faitero almost 8 years ago - 4 comments

#129 - fixes, closes #121 #122 #126 #127

Pull Request - State: closed - Opened by JureZmrzlikar almost 8 years ago - 7 comments

#128 - docs: Add FAQ section, closes #124

Pull Request - State: closed - Opened by tomazc almost 8 years ago - 1 comment

#127 - STAR index

Issue - State: closed - Opened by Faitero almost 8 years ago - 1 comment
Labels: bug

#126 - clusters: Output issue

Issue - State: closed - Opened by nebo56 almost 8 years ago
Labels: bug

#125 - segment: Add suport for GENCODE annotation

Issue - State: closed - Opened by tomazc almost 8 years ago - 7 comments
Labels: enhancement

#124 - peaks: [OSError] 28

Issue - State: closed - Opened by nebo56 almost 8 years ago - 2 comments

#123 - genome: Specify chromosome

Issue - State: closed - Opened by Faitero almost 8 years ago - 1 comment

#122 - peaks: Wrong BED format for identified cross-linked sites

Issue - State: closed - Opened by nebo56 almost 8 years ago - 2 comments
Labels: enhancement

#121 - species: Retrieval of species release

Issue - State: closed - Opened by Faitero almost 8 years ago - 1 comment
Labels: bug

#120 - publish on PyPI

Issue - State: closed - Opened by tomazc almost 8 years ago

#119 - docs: Render on RTD

Pull Request - State: closed - Opened by tomazc almost 8 years ago

#113 - linters: Fix issues, resolves #72

Pull Request - State: closed - Opened by JureZmrzlikar about 8 years ago - 2 comments

#101 - cli: improvements

Pull Request - State: closed - Opened by JureZmrzlikar about 8 years ago - 1 comment

#100 - setup: refactor and write docs for installation, relates to #57

Pull Request - State: closed - Opened by JureZmrzlikar about 8 years ago - 1 comment