Bioinformatics

Student

 Student
First question with score of 1 or more.
Awarded 2127 times.
how is log2foldchange calculated in DESeq2
Awarded 8 hours ago
How can I convert a BED file to GTF/GFF with gene_ids?
Awarded Dec 3 at 7:16
Generate VCF from different .bam files with different chromosome names
Awarded Dec 2 at 22:11
stacked barplot with error bars
Awarded Dec 1 at 4:10
Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index
Awarded Nov 30 at 12:31
bwa mem hangs after a few thousand reads
Awarded Nov 29 at 2:57
What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
Awarded Nov 28 at 21:28
Energy error margin for protein structures
Awarded Nov 25 at 13:49
Eigen phred score interpretation
Awarded Nov 23 at 14:26
Where to access the WGCNA tutorial documents: Horvath lab site down
Awarded Nov 23 at 2:34
(Complete) Stuctural Models of Antibodies: Combining Fc and Fab from pdb to Build Hinge Region? Or what?
Awarded Nov 21 at 7:28
Get a certain gene sequence from bam/vcf and reference
Awarded Nov 20 at 0:33
Sequence Alignment for sequences with the same length
Awarded Nov 16 at 1:18
Producing just network files from BiG-SCAPE
Awarded Nov 15 at 18:27
Confirming Identity of clone in Phylogeny
Awarded Nov 15 at 13:16
Mitochondrial genes - TPM calculation bulk RNA-Seq
Awarded Nov 15 at 8:04
Identification of metabolites through spectral library search
Awarded Nov 11 at 4:45
Racon: empty overlap set!
Awarded Nov 6 at 10:42
Downloading a list of all RCSB-PDB entries
Awarded Nov 5 at 15:56
Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?
Awarded Nov 5 at 14:35
(post deleted or otherwise unavailable)
Awarded Nov 4 at 12:05
What are some good miRNA databases?
Awarded Nov 4 at 1:58
Blastn through NCBIWWW not giving any results, as opposed to the online BLAST
Awarded Nov 1 at 17:33
retrieving past BLAST requests in bioPython
Awarded Nov 1 at 4:32
Adding step size to cross validation in Python package lifelines
Awarded Nov 1 at 4:32
Standardizing Variant IDs best practise
Awarded Oct 29 at 16:26
How to make a POST "vep/:species/region" request that is able to accomodate multiple alternate alleles for a single variant?
Awarded Oct 29 at 7:17
BioPython SeqIO fails with Invalid Alphabet found
Awarded Oct 27 at 21:04
bcbio run not running samples in parallel
Awarded Oct 26 at 15:01
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
Awarded Oct 26 at 3:15
How to create a phylogenetic tree from diverse mitochondrial genomes
Awarded Oct 23 at 11:17
LD clump GRCh38 GWAS results
Awarded Oct 20 at 19:11
Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol
Awarded Oct 19 at 23:18
Renumbering atoms in PDB using OpenBabel
Awarded Oct 19 at 11:03
Cannot obtain alignment summary after running Bowtie2
Awarded Oct 18 at 21:05
How can I incorporate wildcards in Snakemake in an R script?
Awarded Oct 18 at 0:48
Making a DNAStringSet object
Awarded Oct 17 at 13:12
GWAS in python?
Awarded Oct 17 at 3:20
1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?
Awarded Oct 17 at 3:15
Is it possible to, all in memory without writing a file, given a list of AlignedSegments and a bam header, build a bam, index and get coverage?
Awarded Oct 14 at 13:56
Converting VCF format to text for use with PLINK and understanding column mapping
Awarded Oct 13 at 0:10
Find protein in DNA sequences with arbitrary encoding and possible frameshifts
Awarded Oct 12 at 11:30
How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?
Awarded Oct 10 at 0:21
How to interpret a GenomeScope plot?
Awarded Oct 5 at 11:47
Generating CIGAR strings for MSA with reference
Awarded Sep 30 at 13:48
Merge fragment reads
Awarded Sep 29 at 10:18
(post deleted or otherwise unavailable)
Awarded Sep 28 at 11:57
tensorQTL interaction issue
Awarded Sep 28 at 3:16
Align two different structures with respect to their active sites or heme cofactor
Awarded Sep 27 at 13:27
Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences
Awarded Sep 25 at 12:55
Is a classification tree appropriate method to use for my project?
Awarded Sep 23 at 10:10
Do we design primers for single stranded DNA with same criteria as we do for double stranded DNA?
Awarded Sep 21 at 12:08
Changing transparency of markers in Chimera X
Awarded Sep 20 at 1:34
Why does DNABert use overlapping k-mers as input?
Awarded Sep 19 at 16:40
I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header
Awarded Sep 18 at 13:20
How to find an unidentified splicing variant of a protein?
Awarded Sep 15 at 20:41
How do cellranger and cellbender call cells? What is the difference between them?
Awarded Sep 15 at 20:33
What kind of analysis is practically done on GSE data files?
Awarded Sep 15 at 20:27
Difference in Calculation through GEO2R and difference in Article
Awarded Sep 15 at 16:16
how to search and calculate occurence of certain word (like TAA) in fastafile
Awarded Sep 15 at 16:07
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