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1,066 results • Page
2 of 22
Sort: Votes
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Views
Votes
Replies
8
votes
6
replies
639
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
27 days ago by
jiao
▴ 40
8
votes
5
replies
5.7k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
10
replies
751
views
bash script
whole-genome-sequencing
updated 17 days ago by
Ram
43k • written 24 days ago by
bestone
▴ 30
8
votes
3
replies
373
views
How to extract rows with specific values in R for all the columns?
R
29 days ago by
Lakshmi
▴ 20
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 29 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 17 days ago by
e.r.zakiev
▴ 210 • written 16 months ago by
liorglic
★ 1.4k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 15 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 24 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
15 days ago by
Ram
43k
8
votes
16
replies
936
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 6 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
8
votes
8
replies
628
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
Aaliya
▴ 10
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 23 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
2
replies
799
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
27 days ago by
David Langenberger
11k
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 13 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 7 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
7
replies
1.5k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 17 days ago by
Dunois
★ 2.5k • written 18 days ago by
AdviceSeeker
• 0
7
votes
7
replies
589
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 20 days ago by
Matthias Zepper
4.6k • written 20 days ago by
4fzcgueyp5
• 0
7
votes
8
replies
681
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 20 days ago by
spen
▴ 40 • written 23 days ago by
MBarcelo
▴ 40
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 15 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 15 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 15 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
2
replies
284
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 9 days ago by
geneontologyhelp
▴ 390 • written 10 days ago by
catherine.teyssier
• 0
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 16 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 16 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
6
replies
518
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
11 days ago by
analyst
▴ 30
7
votes
8
replies
692
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
28 days ago by
Riq
▴ 50
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 21 days ago by
e.r.zakiev
▴ 210 • written 4.3 years ago by
kevin.stachelek
▴ 80
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 16 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 15 days ago by
Ram
43k • written 3.9 years ago by
mbk0asis
▴ 680
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 15 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 24 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 14 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 27 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 16 days ago by
Ram
43k • written 5.2 years ago by
mohammedtoufiq91
▴ 250
6
votes
3
replies
198
views
Interpretting IGV output
IGV
updated 10 days ago by
Carlo Yague
8.7k • written 10 days ago by
analyst
▴ 30
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 15 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 15 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 23 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
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 14 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 15 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 15 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 15 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
23 days ago by
firestar
★ 1.6k
6
votes
8
replies
592
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 15 days ago by
dariober
14k • written 17 days ago by
manaswiniparija3
▴ 40
6
votes
0
replies
201
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
17 days ago by
Biostar
2.7k
5
votes
5
replies
565
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 23 days ago by
noodle
▴ 580 • written 24 days ago by
a615ebfb
▴ 40
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 22 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
16
replies
687
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
3 days ago by
Ruqaiya
• 0
5
votes
3
replies
251
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by
Lluís R.
★ 1.2k • written 2 days ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
4
replies
349
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
16 days ago by
Spring
• 0
1,066 results • Page
2 of 22
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
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