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240 results • Page
1 of 5
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76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
14 hours ago by
Kevin Blighe
87k
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 6 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
0
votes
14
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 1 day ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 5 days ago by
ATpoint
82k • written 6 days ago by
BioinfGuru
★ 1.7k
3
votes
13
replies
638
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 day ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
11
votes
12
replies
939
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 6 days ago by
Ram
43k • written 6 days ago by
iamsmor
• 0
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 6 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
4
votes
11
replies
490
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 1 day ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
0
votes
10
replies
388
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
1
vote
10
replies
873
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
21 hours ago by
DKA
▴ 40
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
3
votes
9
replies
401
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
2
votes
9
replies
811
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
1
vote
8
replies
722
views
Adding CB tag to bam file
samtools
bam
updated 8 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 5 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
0
votes
8
replies
291
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 6 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
3
votes
8
replies
447
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 11 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
7
votes
7
replies
5.8k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 11 minutes ago by
rohitsatyam102
▴ 840 • written 6.1 years ago by
smallfish
▴ 10
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
4
votes
7
replies
366
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 7 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 6 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
2
votes
7
replies
811
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 6 days ago by
ATpoint
82k • written 7.1 years ago by
boymin2020
▴ 80
7
votes
6
replies
457
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
4 days ago by
analyst
▴ 30
3
votes
6
replies
639
views
Ciriquant not configuring hisat2 indexed files
ciriquant
3 days ago by
Atul K.
• 0
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 6 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
0
votes
6
replies
290
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 4 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
5
replies
681
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
2
votes
5
replies
515
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Giorgio
• 0
0
votes
5
replies
242
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 3 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
8
votes
5
replies
5.0k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
1
vote
5
replies
250
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
1
vote
5
replies
306
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
2 days ago by
anasjamshed
▴ 120
1
vote
5
replies
586
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 1 day ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
1
vote
5
replies
693
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 6 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
rrehimi
• 0
2
votes
5
replies
437
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 5 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
3
votes
5
replies
538
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
3 days ago by
n_navy
• 0
1
vote
5
replies
555
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Luka
• 0
3
votes
5
replies
247
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 3 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
0
votes
5
replies
279
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
5
votes
4
replies
618
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
6 days ago by
BioinfGuru
★ 1.7k
240 results • Page
1 of 5
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by
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141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
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82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
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cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
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Comment: Why gatk VariantAnnotator required bam and coverage files
by
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• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
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141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
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the javascript in your html is deprecated or your firefox is just tool old.
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by
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161k
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▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
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Assa Yeroslaviz
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I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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