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238 results • Page
1 of 5
Sort: Votes
Rank
Views
Votes
Replies
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
13 hours ago by
Kevin Blighe
87k
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
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
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
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
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 17 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
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
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
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
8
votes
5
replies
5.0k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 6 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
6
replies
456
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
4 days ago by
analyst
▴ 30
7
votes
2
replies
247
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 6 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
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
6
votes
3
replies
169
views
Interpretting IGV output
IGV
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
analyst
▴ 30
5
votes
3
replies
704
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 6 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
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
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
5
votes
4
replies
616
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
1 day ago by
kirillkirilenko
▴ 40
4
votes
7
replies
361
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 6 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
4
votes
11
replies
487
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 6 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
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
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 hour ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
8
replies
439
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 10 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
3
replies
711
views
KissDE and batch effect
kissDE
kissplice
3 days ago by
david.b.rombaut
▴ 10
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
3
votes
3
replies
206
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Mariana
▴ 10
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 6 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 6 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
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
3
votes
9
replies
396
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
3
votes
6
replies
634
views
Ciriquant not configuring hisat2 indexed files
ciriquant
3 days ago by
Atul K.
• 0
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
3
votes
3
replies
207
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
3
votes
13
replies
638
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 23 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 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
3
votes
3
replies
182
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
c_u
▴ 520
3
votes
2
replies
266
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
3 days ago by
kristiewyleung
• 0
3
votes
4
replies
650
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
3 days ago by
rahu
• 0
3
votes
3
replies
500
views
Korean human genome reference file
GWAS
reference
imputation
6 days ago by
SeoGyun
• 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
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
3
votes
0
replies
109
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 6 days ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
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
2
votes
5
replies
436
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
238 results • Page
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RSeQC Output from infer_experiment.py - what does it mean?
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Comment: SRA to BAM
Answer: What Is A "Spot" In Sra Format
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Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
jkim
▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question
by
bk11
★ 2.3k
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?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 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
GenoMax
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…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 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?
by
Assa Yeroslaviz
★ 1.8k
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…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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