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1,065 results • Page 2 of 22
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8
votes
8
replies
628
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 7 days ago by 14k • written 9 days ago by ▴ 10
8
votes
6
replies
640
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
28 days ago by jiao ▴ 40
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
3
replies
376
views
How to extract rows with specific values in R for all the columns?
R
29 days ago by Lakshmi ▴ 20
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 43k • written 3.5 years ago by ▴ 240
8
votes
10
replies
752
views
bash script
whole-genome-sequencing
updated 17 days ago by 43k • written 24 days ago by ▴ 30
8
votes
2
replies
802
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
8
votes
5
replies
5.7k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 23 days ago by 43k • written 6.5 years ago by ★ 1.6k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 17 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
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 • 0 • written 3.4 years ago by ▴ 40
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 3.0k • written 24 months ago by ▴ 230
8
votes
16
replies
936
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 6 days ago by ★ 2.4k • written 8 weeks ago by • 0
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 43k • written 5.1 years ago by ▴ 100
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 15 days ago by 43k • written 3.9 years ago by ▴ 680
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 6.4k • written 16 months ago by ▴ 130
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 16 days ago by • 0 • written 6 months ago by ▴ 50
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 43k • written 2.0 years ago by ▴ 60
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 ▴ 850 • written 6.1 years ago by ▴ 10
7
votes
7
replies
590
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 4.6k • written 20 days ago by • 0
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 43k • written 21 months ago by ▴ 20
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 21 days ago by ▴ 210 • written 4.3 years ago by ▴ 80
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 ★ 2.5k • written 18 days ago by • 0
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 15 days ago by 43k • written 6.1 years ago by ▴ 120
7
votes
2
replies
285
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 9 days ago by ▴ 390 • written 10 days ago by • 0
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 15 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
8
replies
693
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
28 days ago by Riq ▴ 50
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 43k • written 4.9 years ago by ▴ 30
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
681
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 20 days ago by ▴ 40 • written 23 days ago by ▴ 40
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 24 days ago by • 0 • written 3.9 years ago by ▴ 120
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 27 days ago by 43k • written 2.6 years ago by ★ 1.9k
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 16 days ago by 43k • written 5.2 years ago by ▴ 40
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 43k • written 5.0 years ago by ▴ 140
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 • 0 • written 4.6 years ago by ▴ 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 43k • written 9.6 years ago by ▴ 100
6
votes
3
replies
198
views
Interpretting IGV output
IGV
updated 10 days ago by 8.7k • written 10 days ago by ▴ 30
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 15 days ago by 43k • written 5.3 years ago by ▴ 120
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 43k • written 6.1 years ago by ▴ 170
6
votes
0
replies
202
views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
17 days ago by Biostar 2.7k
6
votes
8
replies
593
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 15 days ago by 14k • written 17 days ago by ▴ 40
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics 10x
23 days ago by firestar ★ 1.6k
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 43k • written 5.2 years ago by ▴ 250
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 43k • written 4.7 years ago by ▴ 60
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 43k • written 7.0 years ago by ▴ 80
5
votes
3
replies
409
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 21 days ago by 142k • written 21 days ago by ▴ 20
5
votes
16
replies
689
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
3 days ago by Ruqaiya • 0
5
votes
3
replies
333
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 21 days ago by ★ 3.8k • written 22 days ago by ★ 5.3k
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
5
votes
3
replies
252
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by ★ 1.2k • written 2 days ago by • 0
1,065 results • Page 2 of 22
Recent Votes
A: Iterating through paired-end reads in samtools / pysam
Answer: Where Can I Download Some Bam Files?
Download SAM/BAM files from SRA takes ages!!!
Comment: Bedtools merge minimum overlap?
Convert sra to bam file error handling
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
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Recent Replies
Comment: HOMER on AWS by clairechung112 • 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly by clairechung112 • 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
Comment: Bedtools merge minimum overlap? by Alex Reynolds 35k
Note that, in place of `sort-bed - | uniq -`, you can pass the `--unique` option to `sort-bed`. The input is not strictly a BED6 file, but…
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…
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