Ecosyste.ms: Issues

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GitHub / loosolab/TOBIAS issues and pull requests

#298 - Release 0.17.1

Pull Request - State: closed - Opened by hschult 2 months ago

#297 - pip install and cython compile errors

Issue - State: closed - Opened by tjparnell 3 months ago - 4 comments
Labels: bug

#296 - Conduct TOBIAS on CUT&RUN data

Issue - State: closed - Opened by YangzhenyuGao 3 months ago - 1 comment

#295 - Stuck at Estimating normalization factors (ATACorrect)

Issue - State: closed - Opened by eglsdl 3 months ago - 1 comment

#294 - bindetect error

Issue - State: open - Opened by xiasijian 3 months ago - 8 comments
Labels: Stale

#293 - Creating motif2gene_mapping.txt file

Issue - State: closed - Opened by ancient-learner 5 months ago - 2 comments
Labels: Stale

#292 - Including more normalisation methods for the reads

Issue - State: closed - Opened by arodel21 5 months ago - 2 comments

#291 - No common contigs left to run ATACorrect on

Issue - State: closed - Opened by arodel21 5 months ago - 2 comments

#290 - The output of BINDectect about much time points ATAC data

Issue - State: closed - Opened by lay-lei 6 months ago - 2 comments
Labels: Stale

#289 - Finding TF binding site and Motif in specific peaks

Issue - State: closed - Opened by JestlinNg 6 months ago - 2 comments

#287 - TOBIAS BINDetect error in finding some regions

Issue - State: closed - Opened by rmizeret 6 months ago

#286 - Help with BINDetect KeyError

Issue - State: closed - Opened by JestlinNg 6 months ago - 4 comments

#285 - BINDECT warning

Issue - State: closed - Opened by StevenBai97 6 months ago - 1 comment

#284 - ValueError: The data contains non-finite values

Issue - State: closed - Opened by lufuhao 7 months ago - 2 comments
Labels: Stale

#283 - BINDetect output contains not TF clusters

Issue - State: closed - Opened by mohobein 7 months ago - 2 comments
Labels: Stale

#282 - CreateNetwork empty output

Issue - State: closed - Opened by asundaresan1 7 months ago - 2 comments

#281 - Tuning of bound/unbound tresholds

Issue - State: closed - Opened by Fernandobec 7 months ago - 2 comments
Labels: Stale

#280 - Dev

Pull Request - State: closed - Opened by mohobein 7 months ago

#279 - Dev

Pull Request - State: closed - Opened by hschult 7 months ago

#278 - Auto close pr and issue

Pull Request - State: closed - Opened by hschult 7 months ago

#277 - bugfixes and submerge added

Pull Request - State: closed - Opened by mohobein 7 months ago

#276 - Comparability of footprint scores

Issue - State: closed - Opened by rejo27 8 months ago - 4 comments

#274 - Conda/Mamba bioconda installation fails

Issue - State: closed - Opened by augeas 8 months ago - 2 comments

#273 - Healp with CreateNetwork edges.txt interpretation

Issue - State: closed - Opened by c2b2pss 9 months ago - 3 comments
Labels: Stale

#272 - Differential accessibility..., anyway

Issue - State: closed - Opened by lefterov 9 months ago - 1 comment

#268 - added new subcommand to merge TFBS in a subset of regions

Pull Request - State: closed - Opened by mohobein 10 months ago

#267 - Installation problem - solving environment

Issue - State: closed - Opened by sngholee 10 months ago - 1 comment

#266 - BINDetect warning and error

Issue - State: closed - Opened by peryq 10 months ago - 3 comments

#265 - Hi, I have the following three questions for CreateNetwork:

Issue - State: closed - Opened by hyBio 10 months ago - 3 comments
Labels: Stale

#264 - bam and -peaks bed file in ATACorrect

Issue - State: closed - Opened by 31474molly 10 months ago - 4 comments
Labels: Stale

#263 - Difference between --signals and --peaks

Issue - State: closed - Opened by archieandrews10 10 months ago - 2 comments
Labels: Stale

#262 - Threshold for bounded/unbounded TFs ?

Issue - State: closed - Opened by matteozoia4 10 months ago - 2 comments
Labels: Stale

#261 - Field names in bed output

Issue - State: closed - Opened by elia427 11 months ago - 2 comments

#260 - Empty output from CreateNetwork

Issue - State: closed - Opened by swethas112 11 months ago - 3 comments
Labels: Stale

#259 - BINDetect new adjustText error

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

#257 - Bindetect

Pull Request - State: closed - Opened by hschult 11 months ago
Labels: enhancement

#256 - changing clustering threshold in bindetect

Issue - State: closed - Opened by sleepryansleep 11 months ago - 4 comments
Labels: Stale

#255 - PlotChanges error

Issue - State: closed - Opened by swethas112 12 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 about 1 year ago

#253 - Question Regarding the Basis of Motif Logo Creation

Issue - State: closed - Opened by Myrtle-bio about 1 year ago - 2 comments
Labels: Stale

#252 - The data contains non-finite values.

Issue - State: closed - Opened by yhj-j about 1 year ago - 5 comments
Labels: Stale

#250 - Original TOBIAS Manuscript Figure 2--Nature Communications volume 11, Article number: 4267 (2020)

Issue - State: closed - Opened by c2b2pss about 1 year ago - 2 comments
Labels: Stale

#248 - BINDetect not giving out error when the motif file is "deformed"

Issue - State: closed - Opened by johannesnicolaus about 1 year ago - 3 comments
Labels: Stale

#247 - BINDdetect vs plotHeatmap

Issue - State: closed - Opened by mbergsland about 1 year ago - 4 comments
Labels: Stale

#246 - release 0.16.1

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

#245 - Error when plotting comparison of cutsite signals

Issue - State: open - Opened by elia427 about 1 year ago

#244 - module 'matplotlib.cbook' has no attribute 'mplDeprecation'

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

#243 - BINDetect "ERROR IN REGION"

Issue - State: closed - Opened by liz-is over 1 year ago - 3 comments
Labels: bug

#241 - batch effect

Issue - State: closed - Opened by drosop over 1 year ago - 4 comments
Labels: Stale

#238 - Create Newtork

Issue - State: closed - Opened by Rajashree93 over 1 year ago - 1 comment

#237 - About 0-based or 1-based?

Issue - State: closed - Opened by tzhu-bio over 1 year ago - 2 comments
Labels: question

#236 - BINDetect .bed is not proper bed format

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

#235 - TOBIAS ATACorrect fails on some datasets, without any error message

Issue - State: closed - Opened by liz-is over 1 year ago - 5 comments
Labels: Stale

#234 - Memory issue BINDetect Module

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

#233 - "change" field in bindetect_results

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

#232 - Using Shifted .BED Files for ATACorrect?

Issue - State: closed - Opened by ATACSeq-Qs over 1 year ago - 4 comments
Labels: question

#231 - Footprint depth calculation

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

#230 - Question about BinDetect log

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

#227 - Correct matplotlib version for BINDetect?

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

#212 - Clustergram --- "(Clusters below threshold are colored)"

Issue - State: closed - Opened by c2b2pss almost 2 years ago - 10 comments
Labels: Stale

#211 - Inconsistencies between BINDetect volcanoplot and PlotAggregate outputs...

Issue - State: closed - Opened by dmsalsgh97 almost 2 years ago - 4 comments

#209 - Using TOBIAS without BAMs

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

#208 - BINDetect: --peaks merged_peaks_annotated.bed

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

#206 - Sequencing depth / coverage

Issue - State: closed - Opened by adelosan521 almost 2 years ago - 1 comment

#205 - Questions about dealing with snATAC-seq data with multipel samples.

Issue - State: closed - Opened by dmsalsgh97 almost 2 years ago - 2 comments
Labels: question

#204 - TOBIAS_snakemake error -- test_data run fails

Issue - State: closed - Opened by c2b2pss almost 2 years ago - 1 comment

#202 - Is TOBIAS suitable for CUT&Tag of H3K27ac for footprinting detection?

Issue - State: closed - Opened by xflicsu almost 2 years ago - 2 comments
Labels: question

#201 - CreateNetwork with Motifs from Protein-Protein Pair Binding

Issue - State: closed - Opened by sufyazi almost 2 years ago - 2 comments
Labels: question

#200 - Having issue with ploting track.

Issue - State: closed - Opened by mano2991 almost 2 years ago - 5 comments
Labels: bug

#199 - RuntimeError: The data contains non-finite values.

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

#198 - Where is this output generated from and other BINDetect output questions?

Issue - State: closed - Opened by c2b2pss almost 2 years ago - 1 comment

#197 - Installation issue: pyBigWig can't be installed

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

#196 - Contact

Issue - State: closed - Opened by adelosan521 almost 2 years ago - 1 comment