Ecosyste.ms: Issues

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GitHub / drisso/zinbwave issues and pull requests

#73 - zinbsurf taking forever

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

#73 - zinbsurf taking forever

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

#70 - Sample 3 has only 0 counts!

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

#70 - Sample 3 has only 0 counts!

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

#69 - Meaning of the weights

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

#69 - Meaning of the weights

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

#68 - Clarification on observation weights

Issue - State: closed - Opened by prajkta9 over 3 years ago - 1 comment

#68 - Clarification on observation weights

Issue - State: closed - Opened by prajkta9 over 3 years ago - 1 comment

#67 - Negative values in normalizedValues output

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

#67 - Negative values in normalizedValues output

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

#66 - reducedDim() returns only 0

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

#66 - reducedDim() returns only 0

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

#64 - model and K values in zinbwave + Deseq2

Issue - State: open - Opened by AyanoNomura about 4 years ago - 5 comments

#64 - model and K values in zinbwave + Deseq2

Issue - State: open - Opened by AyanoNomura about 4 years ago - 5 comments

#63 - Error in zinbwave

Issue - State: closed - Opened by ZHIDIHUAYUAN about 4 years ago - 1 comment

#63 - Error in zinbwave

Issue - State: closed - Opened by ZHIDIHUAYUAN about 4 years ago - 1 comment

#62 - zinbwave on integrated data set

Issue - State: closed - Opened by yeroslaviz about 4 years ago - 1 comment

#62 - zinbwave on integrated data set

Issue - State: closed - Opened by yeroslaviz about 4 years ago - 1 comment

#61 - How to work with duplicates?

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

#61 - How to work with duplicates?

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

#60 - Computing observational weights in the zinbwave function using a sparse matrix

Issue - State: open - Opened by rfarouni over 4 years ago - 5 comments

#60 - Computing observational weights in the zinbwave function using a sparse matrix

Issue - State: open - Opened by rfarouni over 4 years ago - 5 comments

#59 - W2=0 when calculating two latent variables

Issue - State: closed - Opened by vincr04 over 4 years ago - 3 comments

#59 - W2=0 when calculating two latent variables

Issue - State: closed - Opened by vincr04 over 4 years ago - 3 comments

#58 - Latent factors for differential expression

Issue - State: closed - Opened by vincr04 over 4 years ago - 1 comment

#58 - Latent factors for differential expression

Issue - State: closed - Opened by vincr04 over 4 years ago - 1 comment

#57 - Change zinbwave's default value of K

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

#57 - Change zinbwave's default value of K

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

#56 - Documentation error for "observationalWeights"

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

#56 - Documentation error for "observationalWeights"

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

#55 - padjFilter column in edgeR results

Issue - State: closed - Opened by vincr04 over 4 years ago - 1 comment

#55 - padjFilter column in edgeR results

Issue - State: closed - Opened by vincr04 over 4 years ago - 1 comment

#54 - Decreasing log-likelihood with commondispersion = FALSE

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

#54 - Decreasing log-likelihood with commondispersion = FALSE

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

#53 - Recovery of imputed values

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

#53 - Recovery of imputed values

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

#52 - Adding beta parameter when it uses SolveRidgeRegression function

Pull Request - State: closed - Opened by fedeago almost 5 years ago - 3 comments

#52 - Adding beta parameter when it uses SolveRidgeRegression function

Pull Request - State: closed - Opened by fedeago almost 5 years ago - 3 comments

#51 - Index Error

Issue - State: closed - Opened by ChrisAi89 almost 5 years ago - 2 comments

#51 - Index Error

Issue - State: closed - Opened by ChrisAi89 almost 5 years ago - 2 comments

#50 - Scanpy AnnData Object as Input

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

#50 - Scanpy AnnData Object as Input

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

#49 - added 0 element in nleft; this way correct columns are removed from n…

Pull Request - State: closed - Opened by SzMK almost 5 years ago - 4 comments

#49 - added 0 element in nleft; this way correct columns are removed from n…

Pull Request - State: closed - Opened by SzMK almost 5 years ago - 4 comments

#48 - zinbsurf no longer fails for formula ~1 due to lack of drop=FALSE arg…

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

#48 - zinbsurf no longer fails for formula ~1 due to lack of drop=FALSE arg…

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

#47 - Problem generating observational weights (zinbwave_1.8.0)

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

#47 - Problem generating observational weights (zinbwave_1.8.0)

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

#46 - Normalized value negative correlation with bulk

Issue - State: closed - Opened by zji90 about 5 years ago - 4 comments

#46 - Normalized value negative correlation with bulk

Issue - State: closed - Opened by zji90 about 5 years ago - 4 comments

#45 - zinbwave Matrix error

Issue - State: closed - Opened by cstrlln over 5 years ago - 6 comments

#45 - zinbwave Matrix error

Issue - State: closed - Opened by cstrlln over 5 years ago - 6 comments

#44 - zinbwave design matrix

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

#44 - zinbwave design matrix

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

#43 - Bug in computeObservationWeights?

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

#43 - Bug in computeObservationWeights?

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

#42 - ZinbWave + RSEC error

Issue - State: closed - Opened by siyao-liu almost 6 years ago - 1 comment

#42 - ZinbWave + RSEC error

Issue - State: closed - Opened by siyao-liu almost 6 years ago - 1 comment

#41 - Strange BCV plot for 10x data

Issue - State: open - Opened by lazappi almost 6 years ago - 13 comments

#41 - Strange BCV plot for 10x data

Issue - State: open - Opened by lazappi almost 6 years ago - 13 comments

#39 - Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE

Issue - State: closed - Opened by bio-la almost 6 years ago - 1 comment

#39 - Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE

Issue - State: closed - Opened by bio-la almost 6 years ago - 1 comment

#38 - Zinbwave parallelization issue

Issue - State: open - Opened by giovp about 6 years ago - 11 comments

#38 - Zinbwave parallelization issue

Issue - State: open - Opened by giovp about 6 years ago - 11 comments

#37 - So very slow, could you develop speed-ups using, e.g., Rcpp?

Issue - State: closed - Opened by chriscainx about 6 years ago - 3 comments

#37 - So very slow, could you develop speed-ups using, e.g., Rcpp?

Issue - State: closed - Opened by chriscainx about 6 years ago - 3 comments

#36 - zinbwave+Deseq2 Differential expression 10x

Issue - State: closed - Opened by bio-la about 6 years ago - 3 comments

#36 - zinbwave+Deseq2 Differential expression 10x

Issue - State: closed - Opened by bio-la about 6 years ago - 3 comments

#35 - Managing parallelism on cluster

Issue - State: closed - Opened by afinneg2 over 6 years ago - 3 comments

#35 - Managing parallelism on cluster

Issue - State: closed - Opened by afinneg2 over 6 years ago - 3 comments

#34 - Error if add gene-level covariates

Issue - State: open - Opened by rtian30 over 6 years ago - 3 comments

#34 - Error if add gene-level covariates

Issue - State: open - Opened by rtian30 over 6 years ago - 3 comments

#33 - weights must be finite positive values

Issue - State: closed - Opened by ktroule over 6 years ago - 13 comments

#33 - weights must be finite positive values

Issue - State: closed - Opened by ktroule over 6 years ago - 13 comments

#32 - No weights after zinbwave()

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

#32 - No weights after zinbwave()

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

#31 - zinbFit again stops with error

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

#31 - zinbFit again stops with error

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

#30 - Verbose mode prints wrong value of log likelihood

Issue - State: closed - Opened by drisso over 6 years ago - 1 comment
Labels: bug

#30 - Verbose mode prints wrong value of log likelihood

Issue - State: closed - Opened by drisso over 6 years ago - 1 comment
Labels: bug

#29 - normalization with 5000 or 10000 filtered genes

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

#29 - normalization with 5000 or 10000 filtered genes

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

#28 - Can't run zinbwave in R

Issue - State: closed - Opened by yingzhang121 over 6 years ago - 3 comments

#28 - Can't run zinbwave in R

Issue - State: closed - Opened by yingzhang121 over 6 years ago - 3 comments

#27 - Running zinbwave on cluster

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

#27 - Running zinbwave on cluster

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

#26 - Gene loadings

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

#26 - Gene loadings

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

#25 - maximal number of DLLs reached

Issue - State: closed - Opened by bio-la over 6 years ago - 3 comments

#25 - maximal number of DLLs reached

Issue - State: closed - Opened by bio-la over 6 years ago - 3 comments