ratschlab/spladder issues and pull requests

#204 - viz gives error

Issue - State: open - Opened by NextGenSeek about 2 months ago - 2 comments

#203 - update pypi upload

Pull Request - State: closed - Opened by akahles about 2 months ago

#202 - Spladder Prep Yields No Results And No Error Without `--qmode`

Issue - State: closed - Opened by yr542 2 months ago - 1 comment

#201 - spladder test yields IndexError: index 0 is out of bounds for axis 0 with size 0

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

#200 - Save space at merge step

Issue - State: open - Opened by zyh4482 4 months ago - 6 comments

#199 - e2_cov_region in intron_retention output

Issue - State: closed - Opened by perllb 5 months ago - 1 comment

#198 - Computation time

Issue - State: open - Opened by Elisa89m 6 months ago - 1 comment

#197 - fix IndexError from write.py line 89

Pull Request - State: closed - Opened by ShixiangWang 7 months ago - 3 comments

#196 - local variable 'genes2' referenced before assignment

Issue - State: open - Opened by ls233 8 months ago - 4 comments

#195 - how to speed up the merge step of the build utility?

Issue - State: closed - Opened by ls233 8 months ago

#194 - How to estimate PSI of a new input sample on pre-called events

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

#193 - Does SplAdder work with long-read RNA?

Issue - State: closed - Opened by jkmh2 12 months ago - 2 comments

#192 - ValueError Keyword grid

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

#191 - seaborn not found

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

#190 - Execution fails with --psi-min-reads set to specific value

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

#189 - Spladder viz issue: PDF dimensions out of allowed range

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

#188 - Is_annotated always 3 on negative strand

Issue - State: closed - Opened by perllb over 1 year ago - 5 comments

#187 - Interpretation of the differential splicing testing results

Issue - State: open - Opened by sneha100895 over 1 year ago

#186 - Naming of skipped exons in mutually exclusive events is based on exon length not genomic coordinates

Issue - State: open - Opened by rna-guy over 1 year ago

#185 - viz issue

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

#184 - gff on gtf

Issue - State: open - Opened by ntsopoul almost 2 years ago - 1 comment

#183 - About Image output

Issue - State: open - Opened by avrajit almost 2 years ago - 2 comments

#182 - test run mode - TypeError: Indexing elements must be in increasing order

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

#181 - NGS-994: Add Dockerfile

Pull Request - State: closed - Opened by runarfu almost 2 years ago

#180 - qmode collect step for large cohorts

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

#179 - RuntimeWarning: invalid value encountered in subtract

Issue - State: open - Opened by kate-stankiewicz almost 2 years ago - 2 comments

#178 - TypeError: expected str, bytes or os.PathLike object, not coo_matrix

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

#177 - TypeError: object of type 'Gene' has no len()

Issue - State: closed - Opened by MB571 about 2 years ago - 2 comments

#176 - Use on large cohorts

Issue - State: open - Opened by andrepessoni about 2 years ago - 6 comments

#175 - Test Mode ValueError

Issue - State: open - Opened by JP971 about 2 years ago - 1 comment

#174 - build mode issue

Issue - State: closed - Opened by khksw0403 about 2 years ago - 4 comments

#173 - viz mode issue

Issue - State: open - Opened by selmanurk about 2 years ago - 1 comment

#172 - ValueError: NaN, inf or invalid value detected in endog, estimation infeasible

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

#171 - Index Error during build step

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

#170 - at which stage can i select the confidence threshold?

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

#169 - llvmlite.binding' has no attribute 'get_host_cpu_name

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

#168 - is_annotated column interpretation in splAdder versions 3.x

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

#167 - Spladder accuracy for samples with high multimappers

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

#166 - Testing mode fails despite using the default merging strategy

Issue - State: open - Opened by shepp-hub over 2 years ago - 1 comment

#165 - Viz test not working

Issue - State: closed - Opened by spazm5 over 2 years ago - 3 comments

#164 - Running too slow!

Issue - State: closed - Opened by ifreeman6 over 2 years ago - 2 comments

#163 - Identify novel events with respect to annotation SplAdder v3.0.2

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

#162 - Index error in write.py for psi value

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

#161 - Error in event calling - "Inf" in hdf5

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

#160 - Spladder test stuck

Issue - State: open - Opened by zyh4482 over 2 years ago - 2 comments

#159 - How to incorprate public available spladder gff3 result into a new run?

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

#158 - Different info between "test_results" and "gff3"

Issue - State: closed - Opened by minnie0121 over 2 years ago - 7 comments

#157 - IndexError when running spladder

Issue - State: open - Opened by swu13 over 2 years ago - 7 comments

#156 - ValueError: The first guess on the deviance function returned a nan. This could be a boundary problem and should be reported.

Issue - State: open - Opened by OnkarMulay almost 3 years ago

#155 - UnboundLocalError: local variable 'gene_samples' referenced before assignment

Issue - State: open - Opened by OnkarMulay almost 3 years ago - 17 comments

#154 - splADDER KeyError: 'gene_id'

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

#153 - Index error for spladder build --event-types intron_retention

Issue - State: closed - Opened by wir963 almost 3 years ago - 4 comments

#152 - IndexError during spladder test intron_retension

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

#151 - NameError: name 'get_filename' is not defined

Issue - State: closed - Opened by wir963 almost 3 years ago - 3 comments

#150 - AttributeError: 'Gene' object has no attribute 'symbol'

Issue - State: closed - Opened by wir963 almost 3 years ago - 2 comments

#149 - alt_3prime events AssertionError

Issue - State: closed - Opened by paulojannig almost 3 years ago - 8 comments

#148 - Attribute error

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

#147 - Passing NoneType to string formatting operand

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

#146 - Cannot detect splicing events on many genes

Issue - State: closed - Opened by NancyZhang97 almost 3 years ago - 2 comments

#145 - Old version SplAdder output file --- "Event Files in HDF5 Format" --- what's the meaning of "num_verified" dataset?

Issue - State: closed - Opened by ifreeman6 almost 3 years ago - 7 comments

#144 - RuntimeWarning: invalid value encountered in double_scalars

Issue - State: closed - Opened by gtollefson about 3 years ago - 4 comments

#143 - Conditions/Graph building

Issue - State: closed - Opened by herber4 about 3 years ago - 2 comments

#142 - Spladder Testing issue

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

#141 - Spladder issues in test mode

Issue - State: closed - Opened by OnkarMulay about 3 years ago - 4 comments

#140 - Additional dimension in `verified` dataset in `*counts.hdf5` files

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

#139 - Spladder work for Low read depth

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

#138 - Identify novel events with respect to annotation

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

#137 - Spladder work for low read depth?

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

#136 - Could AS quantification results from a single sample be merged directly downstream?

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

#135 - What is the configuration of the machine required for spladder to combine quantitative results from multiple samples?

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

#134 - Question about zero event detection

Issue - State: closed - Opened by raerose01 over 3 years ago - 4 comments

#133 - Changing colour of spladder viz plots

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

#132 - The iso1 and iso2 fields in the hdf5 files for all the event types except mutex are flipped

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

#131 - Is it possible to get splicing event coordinates on differential test output?

Issue - State: closed - Opened by padilr1 over 3 years ago - 3 comments

#130 - Assertion error

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

#129 - failure at viz mode with --range coordinate

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

#128 - make test error

Issue - State: closed - Opened by Estherrr1997 almost 4 years ago - 8 comments

#127 - How is the PSI value generated in each splice type

Issue - State: closed - Opened by yjzhang2013 almost 4 years ago - 4 comments

#126 - Can't get specific alternative splicing event

Issue - State: closed - Opened by lingziqi8278 almost 4 years ago - 2 comments

#125 - where is the other events all over the genome ?

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

#124 - Which way should I run spladder?

Issue - State: closed - Opened by mhjiang97 over 4 years ago - 4 comments

#123 - No txt/gff output files are generated after spladder builld run

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

#122 - Question about validate-sg-count option

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

#121 - Spladder build: Unable to open Hdf5 file

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

#120 - Running build then test then viz

Issue - State: open - Opened by jjyotikataria over 4 years ago - 3 comments

#119 - Meaning of the headers in the tsv files : output of test mode

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

#118 - Running test mode for all the events

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

#117 - How spladder decides which alternative splicing event to be used as a numerator in psi calculation

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

#116 - Documentation on column headers of txt output

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

#115 - Running viz mode with all events

Issue - State: open - Opened by jjyotikataria over 4 years ago - 1 comment

#114 - Running spladder viz mode

Issue - State: open - Opened by jjyotikataria over 4 years ago - 3 comments

#113 - Example data

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

#112 - Running spladder viz mode

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

#111 - Installation error with pip install and git clone

Issue - State: closed - Opened by JamalEH almost 5 years ago - 1 comment

#110 - sample naming error in spladder output

Issue - State: closed - Opened by PhilippMarkolin almost 5 years ago - 1 comment

GitHub / ratschlab/spladder issues and pull requests