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Showing top results for tag: replicates • reset
0
votes
3
replies
398
views
Cut&Run replicates handling
peakcaller replicates SEACR chipseq
updated 5 months ago by 10k • written 5 months ago by • 0
0
votes
0
replies
243
views
handling bio replicates for chromHMM
replicates chromHMM
5 months ago by Hasan_Daaboul • 0
0
votes
4
replies
686
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
5 months ago by mavy ▴ 10
4
votes
4
replies
788
views
Chip-Seq replicates from different experiments
Chip-seq Normalization Replicates
15 months ago by DavideBrex ▴ 20
3
votes
8
replies
1.1k
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 16 months ago by 146k • written 16 months ago by • 0
4
votes
7
replies
1.0k
views
How to better distribute my replicates between two batches of bulk RNAseq?
replicates RNAseq batch-effect
17 months ago by Victor • 0
5
votes
5
replies
1.3k
views
Biological replicates
biological Replicates
18 months ago by prs ▴ 20
5
votes
4
replies
1.2k
views
No Replicate RNA-Seq (But still biological replicates)
replicates RNA-Seq
18 months ago by foejvs546 ▴ 20
0
votes
2
replies
646
views
DESeq2 replicates in time course data
replicates time-course DESeq2
updated 20 months ago by 44k • written 20 months ago by • 0
0
votes
0
replies
396
views
Much less peaks compared to other replicates
replicates ATAC-seq
20 months ago by zau saa ▴ 150
0
votes
0
replies
354
views
Should I compare Hi-C matrices before or after normalization?
Hi-C Normalization Replicates Pooling Reproducibility
22 months ago by manuel.fernandez ▴ 50
0
votes
0
replies
478
views
Bulk RNAseq experimental design involving in-vitro culturing of primary mouse cells
replicates RNA-seq experimental-design
updated 22 months ago by 44k • written 23 months ago by • 0
0
votes
1
reply
513
views
Microarray analysis
geo2r no microarray replicates
updated 2.3 years ago by 85k • written 2.3 years ago by • 0
0
votes
0
replies
467
views
Replicated samples analysis
repeats replicates
2.3 years ago by valentinavan ▴ 50
1
vote
2
replies
761
views
Understanding Chip-seq data (ENCODE and other resources)
transcription encode factors chip-seq replicates
2.4 years ago by r.kalampaliki • 0
0
votes
2
replies
662
views
Technical replicates of same library samples
Technical calling RNA-seq Variant replicates
updated 2.4 years ago by 85k • written 2.4 years ago by • 0
1
vote
3
replies
3.1k
views
Forum: What counts as a valid biological replicate in single cell RNAseq?
statistics biological replicates scRNA-seq
updated 2.4 years ago by 4.0k • written 2.4 years ago by • 0
3
votes
5
replies
950
views
technical replicates
replicates technical
2.4 years ago by myfam128 • 0
0
votes
7
replies
1.4k
views
Why so much variability in RNA-seq technical replicates?
RNA-seq expression gene replicates technical
2.5 years ago by jaqx008 ▴ 110
0
votes
2
replies
1.9k
views
DESeq2/Differential expression analysis without replicates
No replicates DEG
updated 2.7 years ago by 55k • written 2.7 years ago by ▴ 10
1
vote
1
reply
627
views
RNAseq data with no biological replicates
biological RNA-Seq replicates
2.7 years ago by dew ▴ 10
0
votes
0
replies
488
views
differential expression of mirna
replicates no differential expression mirna
3.0 years ago by e5cf5013 • 0
6
votes
2
replies
993
views
Uneven Biological Replicates for 16S rRNA metabarcoding analysis: Is it justifiable for me to pursue this data?
Analysis statistics replicates microbiome 16S
3.0 years ago by barmonicin ▴ 20
2
votes
2
replies
1.5k
views
scRNA-seq: To merge technical sequencing replicates or not to merge?
technical merging replicates counts RNAseq singlecell
3.0 years ago by Kanai ▴ 10
1
vote
11
replies
2.6k
views
How to perform DE anaysis on a data set in which biological replicates have high varaince?
high replicates biological variance DE
3.1 years ago by Gisele • 0
1
vote
2
replies
806
views
How to calculate the difference between the RNA-Seq individual samples?
comparison expression edgeR replicates R
3.4 years ago by mohammedtoufiq91 ▴ 260
2
votes
1
reply
3.6k
views
How to deal with (combine) technical replicates (FPKM vs Read count data) for RNA-Seq experiments?
RNA-Seq replicates read count gene expression
updated 3.6 years ago by 20 • written 6.6 years ago by ▴ 10
0
votes
0
replies
673
views
How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
3.7 years ago by rimgubaev ▴ 340
1
vote
0
replies
1.3k
views
Combining the original replicates and pseudo-replicates for differential binding analysis?
ChIP-Seq R replicates diffbind
4.2 years ago by maisarasora ▴ 20
4
votes
2
replies
3.6k
views
Is it possible to run DESeq with only two replicates in one group?
RNA-Seq DESeq2 Replicates
updated 4.4 years ago by 85k • written 4.4 years ago by ▴ 400
2
votes
1
reply
1.6k
views
The number of biological replicates and technical replicates in proteomics experiments
proteomics replicates
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 340
3
votes
5
replies
2.2k
views
How to estimate the inter sample and inter replicate correlation coefficient?
RNA-Seq Replicates R2 Correlation coefficients
4.5 years ago by ATCG ▴ 400
6
votes
3
replies
3.3k
views
IDR (Irreproducible Discover Rate) on more than two replicates
IDR ChIP-Seq peak-calling replicates
updated 4.6 years ago by ▴ 40 • written 4.7 years ago by ▴ 60
0
votes
0
replies
782
views
What is the possibility of replicates being different from other replicates of same sample?
microarray replicates mean-error
updated 12 months ago by 44k • written 4.7 years ago by ▴ 310
7
votes
3
replies
3.8k
views
Handling replicates in Chip-seq
ChIP-Seq replicates
updated 4.8 years ago by 20 • written 5.3 years ago by ▴ 100
7
votes
7
replies
2.1k
views
Different number of peaks between biological replicates?
sequencing ChIP-Seq replicates
updated 5.0 years ago by ★ 1.1k • written 5.0 years ago by ▴ 910
7
votes
5
replies
4.4k
views
Which one to use for ChipSeq replicate comparison: Spearman or Pearson
ChIP-Seq correlation replicates genome
updated 5.0 years ago by ★ 1.1k • written 5.0 years ago by ▴ 910
2
votes
7
replies
6.4k
views
Large Variation In Rpkm Values Of Different Biological Replicates From Cufflinks
cufflinks deseq replicates rpkm
updated 5.2 years ago by 20 • written 10.7 years ago by ▴ 30
0
votes
3
replies
1.7k
views
Single Cell RNA Sequencing - replicates pooling and barcoding
scRNA-seq barcode replicates pooling
5.3 years ago by Bolesaem ▴ 10
0
votes
3
replies
802
views
Check for variation between two replicates in transcriptome data
replicates statistical test RNA-seq
5.3 years ago by sagardesai91 ▴ 50
9
votes
5
replies
1.8k
views
macs14 replicates treatment and final wiggle peak files
ChIP-Seq wig-file replicates macs14
updated 5.5 years ago by 12k • written 5.5 years ago by ★ 1.9k
1
vote
1
reply
4.6k
views
Bootstrapping a phylogenetic tree using FastTree
fasttree bootstrapping replicates phylogenetics
5.6 years ago by ginohino • 0
3
votes
0
replies
867
views
Merge MNase-seq bam files from replicates.
next-gen MNase-seq bam-files merge replicates
5.6 years ago by kashiff007 ★ 1.9k
16
votes
14
replies
3.6k
views
Analysis Without Replicates
RNA-Seq Without Replicates
5.9 years ago by Stiofan ▴ 20
1
vote
1
reply
3.1k
views
SRA Database: Samples with Multiple Sequencing Runs Per Sample
SRA technical replicates replicates
6.0 years ago by vlrieg ▴ 20
1
vote
10
replies
4.2k
views
6 follow
DESeq2 for differential expression analysis of RNA-seq datawith few samples per condition?
RNA-Seq deseq2 samples replicates
updated 2.2 years ago by 44k • written 9.0 years ago by ▴ 10
14
votes
9
replies
5.9k
views
6 follow
Replicates for RNA-seq from 1 cell line undergoing different treatments
RNA-Seq Replicates Cell lines
updated 6.4 years ago by ▴ 10 • written 6.8 years ago by ▴ 20
14
votes
9
replies
3.9k
views
How to filter for samples that show good concordance across replicates in DESEQ2 count data from RNA-SEQ?
RNA-Seq DESeq2 replicates prepDE.py R
updated 6.4 years ago by 20k • written 6.4 years ago by ▴ 90
14
votes
7
replies
13k
views
6 follow
Why Cannot Limma Package Do Differential Expression Between Two Samples Without Replication?
affymetrix limma differential-expression replicates
updated 6.8 years ago by 20 • written 11.4 years ago by ▴ 20
46
votes
7
replies
16k
views
7 follow
Rna-Seq Biological Replicates...
rna replicates next-gen sequencing gene
updated 6.8 years ago by ▴ 20 • written 14.5 years ago by ▴ 120
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Recent Replies
Answer: Differential binding analysis between different TFs by Ming Tommy Tang ★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session by Dunois ★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError by Dunois ★ 2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra by Dunois ★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening by Ram 44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data by allingt • 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
Comment: Snakemake expand(): using a helper function (zip) and imputing wildcards? by Jesse ▴ 850
Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
Comment: Extract significant DEGs using Seurat FindConservedMarkers and FindAllMarkers by allingt • 0
In general, you should threshold on the p value that corresponds to the maximum FDR you can accept. In practice, for scRNA-seq data, many g…
Comment: T cell subtype annotation by allingt • 0
I guess reference-based annotation is not an option? In my experience, visualising the expression of canonical markers (I don't know if CD4…
Comment: count number of polymorphic sites among samples in vcf by Ram 44k
I'm not sure if this will work, but you could use `bcftools view` with [include expressions](https://samtools.github.io/bcftools/bcftools.h…
Comment: count number of polymorphic sites among samples in vcf by Pierre Lindenbaum 164k
> However, I want to exclude sites where all of the individuals have a single alternative allele (or a mix of either one alternative allele…
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