Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / loosolab/TOBIAS issues and pull requests
#290 - The output of BINDectect about much time points ATAC data
Issue -
State: open - Opened by lay-lei 30 days ago
#289 - Finding TF binding site and Motif in specific peaks
Issue -
State: open - Opened by JestlinNg about 1 month ago
#288 - How to customize the colors of the profile plots of `TOBIAS PlotAggregate`?
Issue -
State: closed - Opened by danli349 about 2 months ago
- 1 comment
#287 - TOBIAS BINDetect error in finding some regions
Issue -
State: closed - Opened by rmizeret about 2 months ago
#286 - Help with BINDetect KeyError
Issue -
State: closed - Opened by JestlinNg about 2 months ago
- 4 comments
#285 - BINDECT warning
Issue -
State: closed - Opened by StevenBai97 about 2 months ago
- 1 comment
#284 - ValueError: The data contains non-finite values
Issue -
State: open - Opened by lufuhao about 2 months ago
- 1 comment
#283 - BINDetect output contains not TF clusters
Issue -
State: open - Opened by mohobein 2 months ago
- 2 comments
Labels: Stale
#282 - CreateNetwork empty output
Issue -
State: closed - Opened by asundaresan1 2 months ago
- 2 comments
#281 - Tuning of bound/unbound tresholds
Issue -
State: closed - Opened by Fernandobec 2 months ago
- 2 comments
Labels: Stale
#280 - Dev
Pull Request -
State: closed - Opened by mohobein 3 months ago
#279 - Dev
Pull Request -
State: closed - Opened by hschult 3 months ago
#278 - Auto close pr and issue
Pull Request -
State: closed - Opened by hschult 3 months ago
#277 - bugfixes and submerge added
Pull Request -
State: closed - Opened by mohobein 3 months ago
#276 - Comparability of footprint scores
Issue -
State: closed - Opened by rejo27 3 months ago
- 4 comments
#275 - Error with BINDetect static plot, AttributeError: 'FancyArrowPatch' object has no property 'add_objects'
Issue -
State: closed - Opened by Freeda2023 4 months ago
- 4 comments
Labels: Stale
#274 - Conda/Mamba bioconda installation fails
Issue -
State: closed - Opened by augeas 4 months ago
- 2 comments
#273 - Healp with CreateNetwork edges.txt interpretation
Issue -
State: closed - Opened by c2b2pss 4 months ago
- 3 comments
Labels: Stale
#272 - Differential accessibility..., anyway
Issue -
State: closed - Opened by lefterov 4 months ago
- 1 comment
#271 - Help needed: How to interpret the output file from "X_aggregate_comparison_bound" with multiple conditions and others...
Issue -
State: closed - Opened by c2b2pss 4 months ago
- 4 comments
Labels: Stale
#270 - fixed problems related to deprecated adjustText parameters #269 #259 etc
Pull Request -
State: closed - Opened by mohobein 5 months ago
#269 - BINDetect - 'Annotation' object has no property 'text_from_points' only for time series
Issue -
State: closed - Opened by sngholee 5 months ago
- 4 comments
#268 - added new subcommand to merge TFBS in a subset of regions
Pull Request -
State: closed - Opened by mohobein 5 months ago
#267 - Installation problem - solving environment
Issue -
State: closed - Opened by sngholee 5 months ago
- 1 comment
#266 - BINDetect warning and error
Issue -
State: closed - Opened by peryq 5 months ago
- 3 comments
#265 - Hi, I have the following three questions for CreateNetwork:
Issue -
State: closed - Opened by hyBio 6 months ago
- 3 comments
Labels: Stale
#264 - bam and -peaks bed file in ATACorrect
Issue -
State: closed - Opened by 31474molly 6 months ago
- 4 comments
Labels: Stale
#263 - Difference between --signals and --peaks
Issue -
State: closed - Opened by archieandrews10 6 months ago
- 2 comments
Labels: Stale
#262 - Threshold for bounded/unbounded TFs ?
Issue -
State: closed - Opened by matteozoia4 6 months ago
- 2 comments
Labels: Stale
#261 - Field names in bed output
Issue -
State: closed - Opened by elia427 6 months ago
- 2 comments
#260 - Empty output from CreateNetwork
Issue -
State: closed - Opened by swethas112 6 months ago
- 3 comments
Labels: Stale
#259 - BINDetect new adjustText error
Issue -
State: closed - Opened by NMaziak 6 months ago
- 1 comment
#258 - How to compare TOBIAS mean footprint scores called for each sample independently?
Issue -
State: closed - Opened by massonix 7 months ago
- 2 comments
#257 - Bindetect
Pull Request -
State: closed - Opened by hschult 7 months ago
Labels: enhancement
#256 - changing clustering threshold in bindetect
Issue -
State: closed - Opened by sleepryansleep 7 months ago
- 4 comments
Labels: Stale
#255 - PlotChanges error
Issue -
State: closed - Opened by swethas112 7 months ago
- 9 comments
#254 - Set numeric_only to True since None is deprecated in newer pandas ver…
Pull Request -
State: closed - Opened by rwiegan 8 months ago
#253 - Question Regarding the Basis of Motif Logo Creation
Issue -
State: closed - Opened by Myrtle-bio 8 months ago
- 2 comments
Labels: Stale
#252 - The data contains non-finite values.
Issue -
State: closed - Opened by yhj-j 8 months ago
- 5 comments
Labels: Stale
#251 - CreateNetwork issue:Subset 1269038 sites to 0 sites with a valid source id in the '--origin' table
Issue -
State: closed - Opened by kai333334 9 months ago
- 2 comments
#250 - Original TOBIAS Manuscript Figure 2--Nature Communications volume 11, Article number: 4267 (2020)
Issue -
State: closed - Opened by c2b2pss 9 months ago
- 2 comments
Labels: Stale
#250 - Original TOBIAS Manuscript Figure 2--Nature Communications volume 11, Article number: 4267 (2020)
Issue -
State: open - Opened by c2b2pss 9 months ago
- 1 comment
#249 - CreateNetwork: the ensembl ID in bed files (by SNAKEMAKE) included isoform
Issue -
State: closed - Opened by KOBE24DUNK 9 months ago
#248 - BINDetect not giving out error when the motif file is "deformed"
Issue -
State: closed - Opened by johannesnicolaus 10 months ago
- 3 comments
Labels: Stale
#247 - BINDdetect vs plotHeatmap
Issue -
State: closed - Opened by mbergsland 10 months ago
- 4 comments
Labels: Stale
#246 - release 0.16.1
Pull Request -
State: closed - Opened by hschult 10 months ago
#245 - Error when plotting comparison of cutsite signals
Issue -
State: open - Opened by elia427 10 months ago
#244 - module 'matplotlib.cbook' has no attribute 'mplDeprecation'
Issue -
State: closed - Opened by liz-is 11 months ago
- 2 comments
#243 - BINDetect "ERROR IN REGION"
Issue -
State: closed - Opened by liz-is 11 months ago
- 3 comments
Labels: bug
#242 - AttributeError: 'module matplotlib.cbook has no attribute 'mplDeprecation' after installing TOBIAS via pip
Issue -
State: closed - Opened by mano2991 11 months ago
- 2 comments
Labels: bug
#241 - batch effect
Issue -
State: closed - Opened by drosop 11 months ago
- 4 comments
Labels: Stale
#240 - ATACorrect error: Peak region was removed at it is either out of bounds or not in the chromosomes given in genome/bam
Issue -
State: closed - Opened by kkohl96 11 months ago
- 3 comments
#239 - Different locus numbers across conditions and Strategies for Multi-Tissue TF Footprint Score Comparison
Issue -
State: closed - Opened by Myrtle-bio 11 months ago
- 6 comments
Labels: Stale
#238 - Create Newtork
Issue -
State: closed - Opened by Rajashree93 12 months ago
- 1 comment
#237 - About 0-based or 1-based?
Issue -
State: closed - Opened by tzhu-bio 12 months ago
- 2 comments
Labels: question
#236 - BINDetect .bed is not proper bed format
Issue -
State: closed - Opened by portbo 12 months ago
- 2 comments
#235 - TOBIAS ATACorrect fails on some datasets, without any error message
Issue -
State: closed - Opened by liz-is about 1 year ago
- 5 comments
Labels: Stale
#234 - Memory issue BINDetect Module
Issue -
State: closed - Opened by ThorstenCodes about 1 year ago
- 2 comments
#233 - "change" field in bindetect_results
Issue -
State: closed - Opened by amwa about 1 year ago
- 1 comment
#232 - Using Shifted .BED Files for ATACorrect?
Issue -
State: closed - Opened by ATACSeq-Qs about 1 year ago
- 2 comments
Labels: question
#231 - Footprint depth calculation
Issue -
State: closed - Opened by tzhu-bio about 1 year ago
- 2 comments
#230 - Question about BinDetect log
Issue -
State: closed - Opened by amwa about 1 year ago
- 3 comments
#229 - Threshold for TF Footprints/Multiple Overlapping Footprints in PlotTracks
Issue -
State: closed - Opened by beginnertobioinformatics about 1 year ago
- 2 comments
#228 - Interpreting BINDetect _bound.bed files + Running CreateNetwork with JASPAR dimers
Issue -
State: closed - Opened by beginnertobioinformatics about 1 year ago
- 6 comments
#227 - Correct matplotlib version for BINDetect?
Issue -
State: closed - Opened by beginnertobioinformatics about 1 year ago
- 2 comments
#226 - 'total_tfbs' column from BinDetect
Issue -
State: closed - Opened by Rajashree93 over 1 year ago
- 1 comment
Labels: question
#225 - ATAC Correct not utlizing total memory
Issue -
State: closed - Opened by shankar2318 over 1 year ago
- 2 comments
#224 - Z score
Issue -
State: closed - Opened by Rajashree93 over 1 year ago
- 1 comment
#223 - motif file format
Issue -
State: closed - Opened by drosop over 1 year ago
- 4 comments
Labels: enhancement
#222 - Footprint Score Normalisation
Issue -
State: closed - Opened by CriticalSci over 1 year ago
- 7 comments
#221 - AttributeError: 'Annotation' object has no property 'text_from_points'
Issue -
State: closed - Opened by zhoujj2013 over 1 year ago
- 1 comment
#220 - What's the meaning of the Column 5 score in the TOBIAS TFBScan output
Issue -
State: closed - Opened by Rivers-Lee over 1 year ago
- 2 comments
#219 - Getting footprint scores at each individual region
Issue -
State: closed - Opened by sebastian-gregoricchio over 1 year ago
- 2 comments
#218 - Predicted location of Tn5 binding
Issue -
State: closed - Opened by xbendl over 1 year ago
- 2 comments
Labels: question
#217 - TOBIAS and RNAseq data integration
Issue -
State: closed - Opened by deep-buddingcoder over 1 year ago
- 5 comments
#216 - FootprintScores runs extremely slow in 0.15.1
Issue -
State: closed - Opened by maxdudek over 1 year ago
- 2 comments
#214 - Is TOBIAS capable of scanning for TFBSs without calculating binding scores?
Issue -
State: closed - Opened by andradejon over 1 year ago
- 2 comments
#212 - Clustergram --- "(Clusters below threshold are colored)"
Issue -
State: closed - Opened by c2b2pss over 1 year ago
- 10 comments
Labels: Stale
#211 - Inconsistencies between BINDetect volcanoplot and PlotAggregate outputs...
Issue -
State: closed - Opened by dmsalsgh97 over 1 year ago
- 4 comments
#209 - Using TOBIAS without BAMs
Issue -
State: closed - Opened by ndejay over 1 year ago
- 3 comments
#208 - BINDetect: --peaks merged_peaks_annotated.bed
Issue -
State: closed - Opened by deep-buddingcoder over 1 year ago
- 2 comments
#207 - ClusterMotif execution using test dataset: error related to gimmemotifs run
Issue -
State: closed - Opened by deep-buddingcoder over 1 year ago
- 3 comments
#206 - Sequencing depth / coverage
Issue -
State: closed - Opened by adelosan521 over 1 year ago
- 1 comment
#205 - Questions about dealing with snATAC-seq data with multipel samples.
Issue -
State: closed - Opened by dmsalsgh97 over 1 year ago
- 2 comments
Labels: question
#204 - TOBIAS_snakemake error -- test_data run fails
Issue -
State: closed - Opened by c2b2pss over 1 year ago
- 1 comment
#202 - Is TOBIAS suitable for CUT&Tag of H3K27ac for footprinting detection?
Issue -
State: closed - Opened by xflicsu over 1 year ago
- 2 comments
Labels: question
#201 - CreateNetwork with Motifs from Protein-Protein Pair Binding
Issue -
State: closed - Opened by sufyazi over 1 year ago
- 2 comments
Labels: question
#200 - Having issue with ploting track.
Issue -
State: closed - Opened by mano2991 over 1 year ago
- 5 comments
Labels: bug
#199 - RuntimeError: The data contains non-finite values.
Issue -
State: closed - Opened by andradejon over 1 year ago
- 6 comments
#198 - Where is this output generated from and other BINDetect output questions?
Issue -
State: closed - Opened by c2b2pss over 1 year ago
- 1 comment
#197 - Installation issue: pyBigWig can't be installed
Issue -
State: closed - Opened by Matthionine over 1 year ago
- 1 comment
#196 - Contact
Issue -
State: closed - Opened by adelosan521 over 1 year ago
- 1 comment
#195 - PlotAggregate output text file
Issue -
State: closed - Opened by gk1610 over 1 year ago
#194 - Update merge_pdfs.py
Pull Request -
State: closed - Opened by kmlr81 over 1 year ago
#193 - Interpreting "all" vs "bound" files
Issue -
State: closed - Opened by adelosan521 over 1 year ago
- 3 comments
#192 - BINDetect throws std::bad_alloc with .jaspar format JASPAR2022 motifs
Issue -
State: closed - Opened by CriticalSci over 1 year ago
- 1 comment
Labels: bug
#191 - Comparing TF ChIP-seq and TOBIAS
Issue -
State: closed - Opened by adelosan521 over 1 year ago
- 1 comment
#190 - Interesting pattern in FP score distribution
Issue -
State: closed - Opened by maxdudek over 1 year ago
- 3 comments
#189 - annotating peak regions for BINDetect
Issue -
State: closed - Opened by PriyaLakr over 1 year ago
- 2 comments
Labels: question
#188 - Error in rule uropa
Issue -
State: closed - Opened by mano2991 over 1 year ago
- 4 comments