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135 results • Page 1 of 3
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3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel R statistics
updated 5 hours ago by 39k • written 4.2 years ago by ▴ 60
7
votes
12
replies
840
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA integrated ATAC-seq
updated 5 days ago by ▴ 180 • written 12 days ago by ▴ 100
1
vote
10
replies
2.5k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment BLAST tBLASTn
updated 3 days ago by 39k • written 4.2 years ago by ▴ 100
3
votes
8
replies
1.7k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 5 days ago by 39k • written 4.6 years ago by • 0
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 14 hours ago by ★ 3.1k • written 5.3 years ago by ▴ 940
7
votes
7
replies
4.3k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 6 hours ago by 39k • written 4.4 years ago by ▴ 80
2
votes
6
replies
999
views
Time series RNA seq design query
RNA-seq time-series deseq2
updated 7 hours ago by 39k • written 18 months ago by • 0
0
votes
6
replies
320
views
Demultiplexing bam file
demultiplexing bam_file Iontorrent
1 day ago by hasani.iut6 ▴ 60
0
votes
6
replies
215
views
how to create correlation matrix R
pearson-correlation R
updated 7 hours ago by 129k • written 13 hours ago by • 0
3
votes
6
replies
537
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
6 days ago by Sowmya Pulapet ▴ 30
0
votes
6
replies
1.0k
views
How do I tell piRNA population suppress TEs in a bed file?
mapping piRNAs TEs
updated 6 days ago by 39k • written 4.8 years ago by ▴ 110
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis Time-series pairwise
updated 6 hours ago by 39k • written 6.7 years ago by ▴ 470
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping R time-series
updated 6 hours ago by 39k • written 5.2 years ago by ★ 4.2k
3
votes
5
replies
342
views
Uniprot API access to download .pdb files
PDB API Python Uniprot
6 days ago by jdrohan • 0
0
votes
5
replies
366
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 4 hours ago by ▴ 800 • written 3 days ago by ▴ 30
0
votes
5
replies
945
views
Bioinformatics conference with possible publication
conference
updated 5 days ago by 39k • written 4.7 years ago by ▴ 550
0
votes
5
replies
697
views
vcftools --weir-fst-pop returns -nan
fst vcftools
updated 13 hours ago by • 0 • written 5 months ago by • 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna cuffdiff
updated 6 days ago by 39k • written 4.7 years ago by ▴ 10
2
votes
5
replies
381
views
Cutadapt error: too many parameters.
cutadapt parallel bash
11 hours ago by DanielEB_fisk • 0
3
votes
4
replies
328
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 8 hours ago by 21k • written 4 days ago by ▴ 20
0
votes
4
replies
499
views
From VCF to BEAGLE format with multiple chromosomes
vcf vcftools beagle gvcf
6 days ago by Begonia_pavonina ▴ 100
0
votes
4
replies
322
views
desgin a primer for CDS
gene pcr
3 days ago by yuxiang • 0
1
vote
4
replies
341
views
Pre-processing for Agilent microarray data?
affymetrix microarray gene agilent rna
updated 2 days ago by • 0 • written 7 days ago by • 0
0
votes
4
replies
273
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap heatmap rna-seq
updated 4 days ago by ★ 1.1k • written 5 days ago by • 0
0
votes
4
replies
253
views
I need help with a methyl array data analysis
methyl_array DMPs DMRs beta_value r
2 days ago by Ahmad ▴ 10
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence time-series
updated 6 hours ago by 39k • written 6.7 years ago by 10k
0
votes
4
replies
783
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series Gene-Expression Biomarkers
updated 7 hours ago by 39k • written 3.1 years ago by • 0
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 6 hours ago by 39k • written 6.8 years ago by ▴ 720
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl ortho ubuntu mysql
updated 6 days ago by 39k • written 5.0 years ago by ▴ 20
0
votes
4
replies
2.1k
views
picard markduplicate output smaller file
picard markduplicates gatk
updated 4 days ago by 39k • written 4.4 years ago by ▴ 190
1
vote
3
replies
670
views
Regular Expression for conversion
Linux grep
updated 6 hours ago by 21k • written 19 months ago by ▴ 10
2
votes
3
replies
861
views
Freebayes command stopped due to lack of space
freebayes SNP-calling
updated 6 days ago by 39k • written 5.0 years ago by • 0
2
votes
3
replies
687
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics plant-gene-analysis
updated 1 hour ago by 39k • written 4.1 years ago by • 0
2
votes
3
replies
258
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
6 days ago by erik.burchard ▴ 10
1
vote
3
replies
754
views
Stratify phylogeny based on variables - e.g. which ST are represented by high % males
phylogeny statistics
updated 4 days ago by 39k • written 4.3 years ago by ▴ 10
0
votes
3
replies
939
views
Sorting by Prefix Reversal (or Flipping Pancakes) approximation
algorithms
updated 5 days ago by 39k • written 4.5 years ago by • 0
0
votes
3
replies
452
views
how to calcul risk score with a prognostic genes
riskscore multivariate analysis prognostic model
updated 3 days ago by • 0 • written 7 months ago by ▴ 30
0
votes
3
replies
249
views
PLINK not converting entire vcf to bed file
vcf plink genome1000 bed
5 days ago by ethan.kreuzer • 0
0
votes
3
replies
172
views
Query qbout single cell sequencing
fastq ScRNA
updated 2 hours ago by 39k • written 1 day ago by • 0
0
votes
3
replies
989
views
Explanation? Read depth, quality, and assembly accuracy in Methylome analysis context
Assembly genome methylation
updated 4 days ago by 39k • written 4.3 years ago by ▴ 10
2
votes
2
replies
767
views
Final year project query
project
updated 5 days ago by 39k • written 4.5 years ago by • 0
0
votes
2
replies
61
views
gatk Hardfilter Error
hardfilter
updated 4 hours ago by 154k • written 4 hours ago by ▴ 10
1
vote
2
replies
235
views
highlight regions in a dot-plot?
figure dotplot alignment synteny
5 days ago by Buffo ★ 2.2k
0
votes
2
replies
221
views
Error in download library file in expression console software
expression microarray console
7 hours ago by Mohammad • 0
0
votes
2
replies
931
views
what do you mean by segment pairs
rna protein
updated 4 days ago by 39k • written 4.4 years ago by ▴ 50
0
votes
2
replies
169
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping Variant-calling masking
updated 1 day ago by 39k • written 1 day ago by ▴ 120
0
votes
2
replies
150
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring gsea r
1 day ago by pg45863 • 0
1
vote
2
replies
277
views
Identifying/Annotating Enhancers
enhancer R ENCODE bedtools
updated 6 days ago by 72k • written 7 days ago by ▴ 40
0
votes
2
replies
267
views
Import or read Snapgene .dna files into R
R .dna snapgene
4 days ago by eggrandio ▴ 40
0
votes
2
replies
265
views
About inconsistent cell counts per samples obtained in small nuclear RNAseq data.
Seurat QC Single-Cell
4 days ago by bk11 ▴ 60
135 results • Page 1 of 3
Recent Votes
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
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Recent Replies
Comment: Unusual FASTQ file by Ram 39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ? by bhumm ▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index by ashleymb1116 • 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index by GenoMax 129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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