Ecosyste.ms: Issues

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GitHub / zhangyuqing/combat-seq issues and pull requests

#44 - ComBat_seq reruns a list rather a matrix if rm=0

Issue - State: open - Opened by flowerdna about 2 months ago

#44 - ComBat_seq reruns a list rather a matrix if rm=0

Issue - State: open - Opened by flowerdna about 2 months ago

#42 - The covariates are confounded

Issue - State: open - Opened by SimonSchlumbohm 11 months ago - 3 comments

#42 - The covariates are confounded

Issue - State: open - Opened by SimonSchlumbohm 11 months ago - 3 comments

#40 - no data rows with required number of counts

Issue - State: open - Opened by Chenjlin28 about 1 year ago

#40 - no data rows with required number of counts

Issue - State: open - Opened by Chenjlin28 about 1 year ago

#39 - A strange problem

Issue - State: open - Opened by zonzero over 1 year ago - 1 comment

#39 - A strange problem

Issue - State: open - Opened by zonzero over 1 year ago - 1 comment

#38 - Plus one (well, I mean more than one) samples

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

#38 - Plus one (well, I mean more than one) samples

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

#37 - ComBat-seq doesn't support 1 sample per batch yet

Issue - State: open - Opened by jianwu1 over 1 year ago

#36 - Combat-seq, Pseudoaligners and DESeq2

Issue - State: open - Opened by pintoa1-mskcc almost 2 years ago

#35 - running combat-seq with DESeq2

Issue - State: open - Opened by Mercilena almost 2 years ago

#34 - scRNAseq - CombatSeq

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

#33 - How to adjust by multiple variables using ComBat-Seq?

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

#30 - Keep getting the error that rows do not match

Issue - State: open - Opened by sameet-sema4 about 3 years ago - 1 comment

#29 - ComBat_seq took a very long time

Issue - State: open - Opened by rongwong1119 about 3 years ago - 11 comments

#28 - Can I Use ComBat-Seq to adjust multigroups RNAseq?

Issue - State: open - Opened by yirenheihei over 3 years ago

#27 - Using ComBat-Seq to adjust for batch effect/ colony ID

Issue - State: open - Opened by mastoldt over 3 years ago

#26 - Multiple corrections

Issue - State: open - Opened by tea-radut over 3 years ago

#25 - Error in qr.default(design) : NA/NaN/Inf in foreign function call (arg 1)

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

#24 - Run combat-seq on continues variable

Issue - State: open - Opened by jeppeseverens over 3 years ago

#23 - Using ComBat-Seq over RSEM estimated counts

Issue - State: open - Opened by ali-kishk almost 4 years ago - 1 comment

#22 - different output after changing group parameter

Issue - State: open - Opened by mikagm almost 4 years ago

#21 - the vignette returns a matrix | array, real data returns a list

Issue - State: open - Opened by AGordonRobertson almost 4 years ago - 1 comment

#20 - ComBat-Seq correction creating very large count values--cannot feed into DESeq2

Issue - State: open - Opened by cdharshika almost 4 years ago - 11 comments

#16 - install issue on R4.02 and R4.03

Issue - State: open - Opened by sundaochun over 4 years ago

#14 - support for multiple cpus?

Issue - State: open - Opened by cjhong over 4 years ago

#13 - combat-seq can set a reference batch like combat?

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

#12 - ComBat-Seq and pseudobulk counts

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

#11 - Install error

Issue - State: closed - Opened by zckoo007 over 4 years ago - 1 comment

#10 - readcount to FPKM

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

#9 - ComBat (negative value) and ComBat_seq (lib-size)

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

#8 - including more than one feature to be corrected

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

#7 - ComBat-seq + DESeq2

Issue - State: closed - Opened by 14lwt1 over 4 years ago - 4 comments

#6 - Error in phi_matrix

Issue - State: closed - Opened by JOUNGCHANGYOUNG almost 5 years ago - 6 comments

#5 - ComBat_seq cannot be found

Issue - State: closed - Opened by Zepeng-Mu almost 5 years ago - 11 comments

#4 - bug in getting adjusted counts matrix

Issue - State: closed - Opened by davidroad almost 5 years ago - 8 comments

#3 - Question concerning further analysis

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

#2 - Working with normalized datasets

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

#1 - Genes reduced after ComBat-seq

Issue - State: closed - Opened by SL1993 about 5 years ago - 1 comment