Ecosyste.ms: Issues

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GitHub / loosolab/TOBIAS issues and pull requests

#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

#195 - PlotAggregate output text file

Issue - State: closed - Opened by gk1610 about 2 years ago

#194 - Update merge_pdfs.py

Pull Request - State: closed - Opened by kmlr81 about 2 years ago

#193 - Interpreting "all" vs "bound" files

Issue - State: closed - Opened by adelosan521 about 2 years ago - 3 comments

#192 - BINDetect throws std::bad_alloc with .jaspar format JASPAR2022 motifs

Issue - State: closed - Opened by CriticalSci about 2 years ago - 1 comment
Labels: bug

#191 - Comparing TF ChIP-seq and TOBIAS

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

#190 - Interesting pattern in FP score distribution

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

#189 - annotating peak regions for BINDetect

Issue - State: closed - Opened by PriyaLakr about 2 years ago - 2 comments
Labels: question

#188 - Error in rule uropa

Issue - State: closed - Opened by mano2991 about 2 years ago - 4 comments

#187 - A few questions on PlotAggregate

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

#186 - BINDetect output question

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

#185 - Error message (updated) during BINDetect

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

#184 - Error Message

Issue - State: closed - Opened by adelosan521 about 2 years ago

#183 - Tools are not running with TOBIAS <Toolname> command

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

#182 - BINDetect failed for differential analysis

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

#181 - Error in rule bindetect

Issue - State: closed - Opened by VenkateshLab about 2 years ago - 4 comments
Labels: bug

#180 - Error at TOBIAS ATACorrect

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

#179 - where is the test_data directory

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

#178 - multiple conditional xx_footprints.bw data to differential motifs

Issue - State: closed - Opened by archanabhardwaj about 2 years ago - 18 comments

#177 - .bam and .fasta have different chromosome lengths.

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

#176 - Error BINDetect at 'Scanning for motif occurrences' step

Issue - State: closed - Opened by slb2006 about 2 years ago - 4 comments
Labels: bug

#175 - error runnning the TOBIAS ATACorrect

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

#174 - Use pre-calculated Tn5 bias?

Issue - State: closed - Opened by maxdudek about 2 years ago - 3 comments
Labels: enhancement

#173 - Test figures

Issue - State: closed - Opened by adelosan521 about 2 years ago - 34 comments

#172 - TF identifying in chromatin peaks

Issue - State: closed - Opened by adelosan521 about 2 years ago - 3 comments

#171 - Inquiry of the statistics test for the TOBIAS BINDetect

Issue - State: closed - Opened by lynnyummy over 2 years ago - 2 comments
Labels: question

#170 - restarting does not continue from where it left

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

#169 - Normalizing footprint scores per TF for a single condition

Issue - State: closed - Opened by nessj216 over 2 years ago - 3 comments

#168 - Bed file with footprint locations

Issue - State: closed - Opened by odovgusha over 2 years ago - 3 comments
Labels: question

#165 - I am not sure how can I get the `.bed` file for `TOBIAS ATACorrect -p`

Issue - State: closed - Opened by danli349 over 2 years ago - 1 comment
Labels: question

#164 - TOBIAS CreateNetwork

Issue - State: closed - Opened by AndressaOL over 2 years ago - 2 comments
Labels: bug, question

#163 - Understanding significance values out of BINDetect

Issue - State: closed - Opened by jordipla over 2 years ago - 1 comment
Labels: question

#162 - Trouble using ClusterMotifs

Issue - State: closed - Opened by is438indu over 2 years ago - 2 comments
Labels: bug

#160 - Can I run BINDetect just on few subset of peaks?

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

#159 - Error with TOBIAS PlotTrack

Issue - State: closed - Opened by loganminhdang over 2 years ago - 5 comments

#158 - Which value is more "raw" in the output of "BINDetect" step?

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

#157 - Peak within footprint region

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

#156 - CreateNetwork

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

#155 - Expected time taken for TOBIAS to run

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

#154 - issue with "TOBIAS CreateNetwork"

Issue - State: closed - Opened by lynnyummy over 2 years ago - 8 comments

#152 - Minimum reccomended read depth?

Issue - State: closed - Opened by kellisfm over 2 years ago - 2 comments
Labels: question

#151 - Is TOBIAS pipeline supporting organisms other than mice and human?

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

#150 - Footprint looks smoothed with less Tn5 cutsites

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

#149 - Read Shifting

Issue - State: closed - Opened by soheilj over 2 years ago - 4 comments
Labels: question

#148 - DNase-seq

Issue - State: closed - Opened by huangyingzhang over 2 years ago - 1 comment
Labels: question

#147 - Differential binding for genotype-treatment interaction

Issue - State: closed - Opened by ikumar2000 over 2 years ago - 3 comments

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

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

#145 - results from time-series and simple comparison differ

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

#144 - Significance on the BIND_DETECT HTML output

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

#143 - BINDetect: chromsome from region "chr*"not found.

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

#142 - ATACorrect ignoring chromosome names with M letter

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

#141 - Difference between bound and unbound

Issue - State: closed - Opened by Danvor over 2 years ago - 2 comments
Labels: question

#140 - BINDetect running indefinitely

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

#139 - Interpreting binding score distribution

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

#138 - Headers of the bed files generated by BIND DETECT

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

#137 - Single-cell ATACseq

Issue - State: closed - Opened by annrosebright almost 3 years ago - 10 comments
Labels: enhancement

#136 - PlotTracks can't plot the gene pattern

Issue - State: closed - Opened by Eric-tsc almost 3 years ago - 12 comments
Labels: enhancement

#135 - Question about CreateNetwork

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

#134 - Meaning of the values in the bias bigwig file

Issue - State: closed - Opened by HYsxe almost 3 years ago - 5 comments
Labels: question

#133 - Use of CreateNetwork

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

#132 - Use TOBIAS with DNAse-seq data

Issue - State: closed - Opened by hy09 almost 3 years ago - 2 comments
Labels: question

#131 - BINDetect gets stuck while loading motifs

Issue - State: closed - Opened by thijs32 almost 3 years ago - 2 comments

#130 - user defined heatmap color in TOBIAS PlotHeatmap

Issue - State: closed - Opened by raunakms almost 3 years ago - 2 comments
Labels: enhancement

#129 - Can be tobias launched on bigwig data rather than bams?

Issue - State: closed - Opened by xbendl almost 3 years ago - 2 comments
Labels: question

#128 - BINdetect, or?

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

#127 - ATACorrect: raise pickle.PicklingError('logger cannot be pickled')

Issue - State: closed - Opened by ro-zeta almost 3 years ago - 8 comments
Labels: bug

#125 - motifs2gene file generation

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

#124 - MOTIFS File Generation

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

#123 - TOBIAS BINDetect

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

#122 - TFBS_score

Issue - State: closed - Opened by ikumar2000 almost 3 years ago - 3 comments
Labels: question

#121 - Minimum size of input peak regions

Issue - State: closed - Opened by Erhei130 almost 3 years ago - 3 comments

#119 - Progress:0%, in parallel problem?

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

#118 - snakemake example_config.yaml pipeline failed in writing all_motifs.txt

Issue - State: closed - Opened by mdu4003 about 3 years ago - 5 comments

#115 - Snakemake pipeline documentation and problem with conda install TOBIAS_ENV

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

#111 - Nfr fragments

Issue - State: closed - Opened by ikumar2000 about 3 years ago - 1 comment
Labels: question

#106 - Customized motif bed files as BINDetect input

Issue - State: closed - Opened by yyc0415 about 3 years ago - 2 comments
Labels: enhancement, Stale

#105 - Can I use Tobias to make non-pairwise comparisons?

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

#104 - Help understanding atacorrect calculation of post-bias variance

Issue - State: closed - Opened by HillJamie about 3 years ago - 1 comment
Labels: question

#98 - Footprinting for multiple tissues.

Issue - State: closed - Opened by tzhu-bio over 3 years ago - 5 comments
Labels: question

#96 - Portability to MNase-seq based assay

Issue - State: closed - Opened by gang-pan over 3 years ago - 3 comments
Labels: question

#93 - BINDetect import error

Issue - State: closed - Opened by anacatalan over 3 years ago - 5 comments

#89 - Question about CreateNetwork

Issue - State: closed - Opened by DittmanC over 3 years ago - 3 comments
Labels: question

#82 - Filter BINDetect results based on volcano plot

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

#53 - ATACorrect Stuck on Estimation of Sequence Bias

Issue - State: closed - Opened by bbraun923 about 4 years ago - 8 comments

#19 - Is it possible to get the list of the TFBS around a gene and its score?

Issue - State: closed - Opened by smallfade over 4 years ago - 4 comments
Labels: documentation, Stale

#12 - What does the columns mean in edges.txt from CreateNetwork?

Issue - State: closed - Opened by smallfade almost 5 years ago - 6 comments
Labels: documentation, enhancement, Stale